Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/gmap-2020-11-20+ds/src/oligoindex_hr.h
Examining data/gmap-2020-11-20+ds/src/cmetindex.c
Examining data/gmap-2020-11-20+ds/src/uintlistpool.c
Examining data/gmap-2020-11-20+ds/src/distant-rna.h
Examining data/gmap-2020-11-20+ds/src/sedgesort.c
Examining data/gmap-2020-11-20+ds/src/get-genome.c
Examining data/gmap-2020-11-20+ds/src/univcoord.h
Examining data/gmap-2020-11-20+ds/src/dynprog_single.c
Examining data/gmap-2020-11-20+ds/src/chrom.h
Examining data/gmap-2020-11-20+ds/src/indexdb-write.c
Examining data/gmap-2020-11-20+ds/src/atoiindex.c
Examining data/gmap-2020-11-20+ds/src/diagnostic.h
Examining data/gmap-2020-11-20+ds/src/path-solve.c
Examining data/gmap-2020-11-20+ds/src/simplepair.h
Examining data/gmap-2020-11-20+ds/src/reader.c
Examining data/gmap-2020-11-20+ds/src/cellpool.h
Examining data/gmap-2020-11-20+ds/src/samread.h
Examining data/gmap-2020-11-20+ds/src/interval.c
Examining data/gmap-2020-11-20+ds/src/result.c
Examining data/gmap-2020-11-20+ds/src/splicestringpool.c
Examining data/gmap-2020-11-20+ds/src/snpindex.c
Examining data/gmap-2020-11-20+ds/src/genome.h
Examining data/gmap-2020-11-20+ds/src/samheader.c
Examining data/gmap-2020-11-20+ds/src/mdprint.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-readtwo.c
Examining data/gmap-2020-11-20+ds/src/genome_canonical.c
Examining data/gmap-2020-11-20+ds/src/listpool.c
Examining data/gmap-2020-11-20+ds/src/ladder.h
Examining data/gmap-2020-11-20+ds/src/intron.h
Examining data/gmap-2020-11-20+ds/src/substring.c
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint8.h
Examining data/gmap-2020-11-20+ds/src/dinucl_bits.c
Examining data/gmap-2020-11-20+ds/src/output.h
Examining data/gmap-2020-11-20+ds/src/sam_sort.c
Examining data/gmap-2020-11-20+ds/src/listpool.h
Examining data/gmap-2020-11-20+ds/src/filestring.c
Examining data/gmap-2020-11-20+ds/src/genome_canonical.h
Examining data/gmap-2020-11-20+ds/src/chrnum.h
Examining data/gmap-2020-11-20+ds/src/diagpool.h
Examining data/gmap-2020-11-20+ds/src/merge-uint4.c
Examining data/gmap-2020-11-20+ds/src/dynprog_genome.h
Examining data/gmap-2020-11-20+ds/src/match.h
Examining data/gmap-2020-11-20+ds/src/doublelist.c
Examining data/gmap-2020-11-20+ds/src/simplepair.c
Examining data/gmap-2020-11-20+ds/src/bool.h
Examining data/gmap-2020-11-20+ds/src/univinterval.h
Examining data/gmap-2020-11-20+ds/src/oligo.c
Examining data/gmap-2020-11-20+ds/src/parserange.c
Examining data/gmap-2020-11-20+ds/src/dynprog.c
Examining data/gmap-2020-11-20+ds/src/list.h
Examining data/gmap-2020-11-20+ds/src/sense.h
Examining data/gmap-2020-11-20+ds/src/diag.h
Examining data/gmap-2020-11-20+ds/src/univdiagpool.h
Examining data/gmap-2020-11-20+ds/src/translation.h
Examining data/gmap-2020-11-20+ds/src/stopwatch.h
Examining data/gmap-2020-11-20+ds/src/fastlog.h
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c
Examining data/gmap-2020-11-20+ds/src/stage3.h
Examining data/gmap-2020-11-20+ds/src/stage3hr.h
Examining data/gmap-2020-11-20+ds/src/filesuffix.h
Examining data/gmap-2020-11-20+ds/src/shortread.h
Examining data/gmap-2020-11-20+ds/src/intron.c
Examining data/gmap-2020-11-20+ds/src/intersect-large.h
Examining data/gmap-2020-11-20+ds/src/intlistpool.c
Examining data/gmap-2020-11-20+ds/src/sequence.c
Examining data/gmap-2020-11-20+ds/src/tableuint.c
Examining data/gmap-2020-11-20+ds/src/regiondb.c
Examining data/gmap-2020-11-20+ds/src/transcript.c
Examining data/gmap-2020-11-20+ds/src/outbuffer.c
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.h
Examining data/gmap-2020-11-20+ds/src/intersect.c
Examining data/gmap-2020-11-20+ds/src/splicetrie.c
Examining data/gmap-2020-11-20+ds/src/merge-uint4.h
Examining data/gmap-2020-11-20+ds/src/gregion.h
Examining data/gmap-2020-11-20+ds/src/request.h
Examining data/gmap-2020-11-20+ds/src/stage2.c
Examining data/gmap-2020-11-20+ds/src/gmapl_select.c
Examining data/gmap-2020-11-20+ds/src/inbuffer.h
Examining data/gmap-2020-11-20+ds/src/littleendian.h
Examining data/gmap-2020-11-20+ds/src/merge-uint8.h
Examining data/gmap-2020-11-20+ds/src/genome-write.c
Examining data/gmap-2020-11-20+ds/src/changepoint.c
Examining data/gmap-2020-11-20+ds/src/regiondb-write.c
Examining data/gmap-2020-11-20+ds/src/chimera.c
Examining data/gmap-2020-11-20+ds/src/resulthr.h
Examining data/gmap-2020-11-20+ds/src/dynprog_genome.c
Examining data/gmap-2020-11-20+ds/src/stage3.c
Examining data/gmap-2020-11-20+ds/src/transcriptome.h
Examining data/gmap-2020-11-20+ds/src/assert.h
Examining data/gmap-2020-11-20+ds/src/stage1hr.h
Examining data/gmap-2020-11-20+ds/src/path-solve.h
Examining data/gmap-2020-11-20+ds/src/indexdb-write.h
Examining data/gmap-2020-11-20+ds/src/segmentpos.c
Examining data/gmap-2020-11-20+ds/src/dynprog_end.h
Examining data/gmap-2020-11-20+ds/src/splice.c
Examining data/gmap-2020-11-20+ds/src/cigar.h
Examining data/gmap-2020-11-20+ds/src/iit_get.c
Examining data/gmap-2020-11-20+ds/src/matchdef.h
Examining data/gmap-2020-11-20+ds/src/hitlistpool.c
Examining data/gmap-2020-11-20+ds/src/matchpool.c
Examining data/gmap-2020-11-20+ds/src/terminal.c
Examining data/gmap-2020-11-20+ds/src/concordance.c
Examining data/gmap-2020-11-20+ds/src/oligoindex_hr.c
Examining data/gmap-2020-11-20+ds/src/indexdb.h
Examining data/gmap-2020-11-20+ds/src/uint8list.c
Examining data/gmap-2020-11-20+ds/src/univdiagdef.h
Examining data/gmap-2020-11-20+ds/src/mapq.h
Examining data/gmap-2020-11-20+ds/src/univinterval.c
Examining data/gmap-2020-11-20+ds/src/popcount.h
Examining data/gmap-2020-11-20+ds/src/genome_sites.c
Examining data/gmap-2020-11-20+ds/src/splice.h
Examining data/gmap-2020-11-20+ds/src/tableuint.h
Examining data/gmap-2020-11-20+ds/src/stage1.h
Examining data/gmap-2020-11-20+ds/src/md5.c
Examining data/gmap-2020-11-20+ds/src/stage1hr.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-access.h
Examining data/gmap-2020-11-20+ds/src/scores.h
Examining data/gmap-2020-11-20+ds/src/genome128_consec.c
Examining data/gmap-2020-11-20+ds/src/stopwatch.c
Examining data/gmap-2020-11-20+ds/src/gmap.c
Examining data/gmap-2020-11-20+ds/src/indexdb.c
Examining data/gmap-2020-11-20+ds/src/datadir.c
Examining data/gmap-2020-11-20+ds/src/stage3hrdef.h
Examining data/gmap-2020-11-20+ds/src/compress.c
Examining data/gmap-2020-11-20+ds/src/regiondb.h
Examining data/gmap-2020-11-20+ds/src/pair.c
Examining data/gmap-2020-11-20+ds/src/ladder.c
Examining data/gmap-2020-11-20+ds/src/genome_sites.h
Examining data/gmap-2020-11-20+ds/src/uint8list.h
Examining data/gmap-2020-11-20+ds/src/segmentpos.h
Examining data/gmap-2020-11-20+ds/src/iit-read-univ.c
Examining data/gmap-2020-11-20+ds/src/smooth.c
Examining data/gmap-2020-11-20+ds/src/kmer-search.h
Examining data/gmap-2020-11-20+ds/src/dynprog_cdna.h
Examining data/gmap-2020-11-20+ds/src/oligo.h
Examining data/gmap-2020-11-20+ds/src/table.c
Examining data/gmap-2020-11-20+ds/src/distant-rna.c
Examining data/gmap-2020-11-20+ds/src/tableuint8.c
Examining data/gmap-2020-11-20+ds/src/iit-read.c
Examining data/gmap-2020-11-20+ds/src/splicetrie_build.h
Examining data/gmap-2020-11-20+ds/src/uinttable_rh.h
Examining data/gmap-2020-11-20+ds/src/dynprog_end.c
Examining data/gmap-2020-11-20+ds/src/table.h
Examining data/gmap-2020-11-20+ds/src/dinucl_bits.h
Examining data/gmap-2020-11-20+ds/src/gsnap.c
Examining data/gmap-2020-11-20+ds/src/cmet.c
Examining data/gmap-2020-11-20+ds/src/iit-write-univ.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-write.h
Examining data/gmap-2020-11-20+ds/src/genomicpos.c
Examining data/gmap-2020-11-20+ds/src/diagdef.h
Examining data/gmap-2020-11-20+ds/src/resulthr.c
Examining data/gmap-2020-11-20+ds/src/iit-write.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-read.h
Examining data/gmap-2020-11-20+ds/src/mdprint.h
Examining data/gmap-2020-11-20+ds/src/maxent_hr.c
Examining data/gmap-2020-11-20+ds/src/outbuffer.h
Examining data/gmap-2020-11-20+ds/src/block.h
Examining data/gmap-2020-11-20+ds/src/bitpack64-incr.c
Examining data/gmap-2020-11-20+ds/src/dynprog.h
Examining data/gmap-2020-11-20+ds/src/uintlistpool.h
Examining data/gmap-2020-11-20+ds/src/samheader.h
Examining data/gmap-2020-11-20+ds/src/bzip2.c
Examining data/gmap-2020-11-20+ds/src/mem.h
Examining data/gmap-2020-11-20+ds/src/bzip2.h
Examining data/gmap-2020-11-20+ds/src/interval.h
Examining data/gmap-2020-11-20+ds/src/output.c
Examining data/gmap-2020-11-20+ds/src/atoi.h
Examining data/gmap-2020-11-20+ds/src/junction.h
Examining data/gmap-2020-11-20+ds/src/changepoint.h
Examining data/gmap-2020-11-20+ds/src/intersect-large.c
Examining data/gmap-2020-11-20+ds/src/block.c
Examining data/gmap-2020-11-20+ds/src/merge-uint8.c
Examining data/gmap-2020-11-20+ds/src/md5.h
Examining data/gmap-2020-11-20+ds/src/separator.h
Examining data/gmap-2020-11-20+ds/src/kmer-search.c
Examining data/gmap-2020-11-20+ds/src/diagnostic.c
Examining data/gmap-2020-11-20+ds/src/knownsplicing.c
Examining data/gmap-2020-11-20+ds/src/segment-search.h
Examining data/gmap-2020-11-20+ds/src/record.h
Examining data/gmap-2020-11-20+ds/src/atoi.c
Examining data/gmap-2020-11-20+ds/src/distant-dna.c
Examining data/gmap-2020-11-20+ds/src/genome.c
Examining data/gmap-2020-11-20+ds/src/indel.h
Examining data/gmap-2020-11-20+ds/src/regiondb-write.h
Examining data/gmap-2020-11-20+ds/src/maxent_hr.h
Examining data/gmap-2020-11-20+ds/src/except.c
Examining data/gmap-2020-11-20+ds/src/maxent.h
Examining data/gmap-2020-11-20+ds/src/boyer-moore.h
Examining data/gmap-2020-11-20+ds/src/knownsplicing.h
Examining data/gmap-2020-11-20+ds/src/dynprog_simd.c
Examining data/gmap-2020-11-20+ds/src/getline.h
Examining data/gmap-2020-11-20+ds/src/parserange.h
Examining data/gmap-2020-11-20+ds/src/mem.c
Examining data/gmap-2020-11-20+ds/src/pairpool.h
Examining data/gmap-2020-11-20+ds/src/genome-write.h
Examining data/gmap-2020-11-20+ds/src/extension-search.h
Examining data/gmap-2020-11-20+ds/src/gsnapl_select.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-incr.h
Examining data/gmap-2020-11-20+ds/src/assert.c
Examining data/gmap-2020-11-20+ds/src/pairpool.c
Examining data/gmap-2020-11-20+ds/src/regiondbdef.h
Examining data/gmap-2020-11-20+ds/src/tableuint8.h
Examining data/gmap-2020-11-20+ds/src/extension-search.c
Examining data/gmap-2020-11-20+ds/src/intlist.c
Examining data/gmap-2020-11-20+ds/src/genome128_consec.h
Examining data/gmap-2020-11-20+ds/src/gsnap_select.c
Examining data/gmap-2020-11-20+ds/src/maxent.c
Examining data/gmap-2020-11-20+ds/src/splicestringpool.h
Examining data/gmap-2020-11-20+ds/src/matchpool.h
Examining data/gmap-2020-11-20+ds/src/bitpack64-read.c
Examining data/gmap-2020-11-20+ds/src/translation.c
Examining data/gmap-2020-11-20+ds/src/univdiagpool.c
Examining data/gmap-2020-11-20+ds/src/iitdef.h
Examining data/gmap-2020-11-20+ds/src/samread.c
Examining data/gmap-2020-11-20+ds/src/genome128_hr.c
Examining data/gmap-2020-11-20+ds/src/orderstat.h
Examining data/gmap-2020-11-20+ds/src/semaphore.h
Examining data/gmap-2020-11-20+ds/src/shortread.c
Examining data/gmap-2020-11-20+ds/src/gbuffer.c
Examining data/gmap-2020-11-20+ds/src/stage3hr.c
Examining data/gmap-2020-11-20+ds/src/complement.h
Examining data/gmap-2020-11-20+ds/src/access.h
Examining data/gmap-2020-11-20+ds/src/reader.h
Examining data/gmap-2020-11-20+ds/src/chimera.h
Examining data/gmap-2020-11-20+ds/src/uint8listpool.h
Examining data/gmap-2020-11-20+ds/src/cpuid.h
Examining data/gmap-2020-11-20+ds/src/pairdef.h
Examining data/gmap-2020-11-20+ds/src/iit-read.h
Examining data/gmap-2020-11-20+ds/src/junction.c
Examining data/gmap-2020-11-20+ds/src/fopen.c
Examining data/gmap-2020-11-20+ds/src/genomicpos.h
Examining data/gmap-2020-11-20+ds/src/gbuffer.h
Examining data/gmap-2020-11-20+ds/src/concordance.h
Examining data/gmap-2020-11-20+ds/src/bigendian.c
Examining data/gmap-2020-11-20+ds/src/splicetrie_build.c
Examining data/gmap-2020-11-20+ds/src/substring.h
Examining data/gmap-2020-11-20+ds/src/segment-search.c
Examining data/gmap-2020-11-20+ds/src/request.c
Examining data/gmap-2020-11-20+ds/src/cellpool.c
Examining data/gmap-2020-11-20+ds/src/iit-read-univ.h
Examining data/gmap-2020-11-20+ds/src/samflags.h
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-heap.h
Examining data/gmap-2020-11-20+ds/src/intlistpool.h
Examining data/gmap-2020-11-20+ds/src/genome128_hr.h
Examining data/gmap-2020-11-20+ds/src/tableint.h
Examining data/gmap-2020-11-20+ds/src/pbinom.c
Examining data/gmap-2020-11-20+ds/src/cigar.c
Examining data/gmap-2020-11-20+ds/src/indexdbdef.h
Examining data/gmap-2020-11-20+ds/src/method.c
Examining data/gmap-2020-11-20+ds/src/except.h
Examining data/gmap-2020-11-20+ds/src/smooth.h
Examining data/gmap-2020-11-20+ds/src/stage2.h
Examining data/gmap-2020-11-20+ds/src/diagpool.c
Examining data/gmap-2020-11-20+ds/src/types.h
Examining data/gmap-2020-11-20+ds/src/uint8table_rh.h
Examining data/gmap-2020-11-20+ds/src/intlist.h
Examining data/gmap-2020-11-20+ds/src/transcript.h
Examining data/gmap-2020-11-20+ds/src/littleendian.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-access.c
Examining data/gmap-2020-11-20+ds/src/compress-write.c
Examining data/gmap-2020-11-20+ds/src/match.c
Examining data/gmap-2020-11-20+ds/src/diag.c
Examining data/gmap-2020-11-20+ds/src/pair.h
Examining data/gmap-2020-11-20+ds/src/uint8listpool.c
Examining data/gmap-2020-11-20+ds/src/sequence.h
Examining data/gmap-2020-11-20+ds/src/uint8table_rh.c
Examining data/gmap-2020-11-20+ds/src/mode.h
Examining data/gmap-2020-11-20+ds/src/univdiag.h
Examining data/gmap-2020-11-20+ds/src/stage1.c
Examining data/gmap-2020-11-20+ds/src/gregion.c
Examining data/gmap-2020-11-20+ds/src/fopen.h
Examining data/gmap-2020-11-20+ds/src/iit_dump.c
Examining data/gmap-2020-11-20+ds/src/datadir.h
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint8.c
Examining data/gmap-2020-11-20+ds/src/indel.c
Examining data/gmap-2020-11-20+ds/src/semaphore.c
Examining data/gmap-2020-11-20+ds/src/iit-write-univ.h
Examining data/gmap-2020-11-20+ds/src/distant-dna.h
Examining data/gmap-2020-11-20+ds/src/pbinom.h
Examining data/gmap-2020-11-20+ds/src/cmet.h
Examining data/gmap-2020-11-20+ds/src/terminal.h
Examining data/gmap-2020-11-20+ds/src/getline.c
Examining data/gmap-2020-11-20+ds/src/iit_store.c
Examining data/gmap-2020-11-20+ds/src/boyer-moore.c
Examining data/gmap-2020-11-20+ds/src/result.h
Examining data/gmap-2020-11-20+ds/src/compress-write.h
Examining data/gmap-2020-11-20+ds/src/univdiag.c
Examining data/gmap-2020-11-20+ds/src/access.c
Examining data/gmap-2020-11-20+ds/src/sedgesort.h
Examining data/gmap-2020-11-20+ds/src/tableint.c
Examining data/gmap-2020-11-20+ds/src/merge-diagonals-heap.c
Examining data/gmap-2020-11-20+ds/src/transcriptome.c
Examining data/gmap-2020-11-20+ds/src/compress.h
Examining data/gmap-2020-11-20+ds/src/dynprog_cdna.c
Examining data/gmap-2020-11-20+ds/src/filestring.h
Examining data/gmap-2020-11-20+ds/src/gmapindex.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-readtwo.h
Examining data/gmap-2020-11-20+ds/src/chrom.c
Examining data/gmap-2020-11-20+ds/src/dynprog_simd.h
Examining data/gmap-2020-11-20+ds/src/dynprog_single.h
Examining data/gmap-2020-11-20+ds/src/samprint.h
Examining data/gmap-2020-11-20+ds/src/doublelist.h
Examining data/gmap-2020-11-20+ds/src/uintlist.h
Examining data/gmap-2020-11-20+ds/src/uintlist.c
Examining data/gmap-2020-11-20+ds/src/uinttable_rh.c
Examining data/gmap-2020-11-20+ds/src/comp.h
Examining data/gmap-2020-11-20+ds/src/indexdb-cat.c
Examining data/gmap-2020-11-20+ds/src/iit-write.h
Examining data/gmap-2020-11-20+ds/src/orderstat.c
Examining data/gmap-2020-11-20+ds/src/samprint.c
Examining data/gmap-2020-11-20+ds/src/intersect.h
Examining data/gmap-2020-11-20+ds/src/mapq.c
Examining data/gmap-2020-11-20+ds/src/chrnum.c
Examining data/gmap-2020-11-20+ds/src/method.h
Examining data/gmap-2020-11-20+ds/src/inbuffer.c
Examining data/gmap-2020-11-20+ds/src/list.c
Examining data/gmap-2020-11-20+ds/src/bigendian.h
Examining data/gmap-2020-11-20+ds/src/gmap_select.c
Examining data/gmap-2020-11-20+ds/src/splicetrie.h
Examining data/gmap-2020-11-20+ds/src/popcount.c
Examining data/gmap-2020-11-20+ds/src/hitlistpool.h
Examining data/gmap-2020-11-20+ds/src/trindex.c
Examining data/gmap-2020-11-20+ds/src/bitpack64-write.c
Examining data/gmap-2020-11-20+ds/src/cpuid.c
FINAL RESULTS:
data/gmap-2020-11-20+ds/src/access.c:781:36: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_allocate_private (Access_T *access, size_t *len, double *seconds, char *filename, size_t eltsize) {
data/gmap-2020-11-20+ds/src/access.c:845:35: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_allocate_shared (Access_T *access, int *shmid, key_t *key, int *fd, size_t *len, double *seconds, char *filename, size_t eltsize) {
data/gmap-2020-11-20+ds/src/access.h:61:36: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_allocate_private (Access_T *access, size_t *len, double *seconds, char *filename, size_t eltsize);
data/gmap-2020-11-20+ds/src/access.h:63:35: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_allocate_shared (Access_T *access, int *shmid, key_t *key, int *fd, size_t *len, double *seconds, char *filename, size_t eltsize);
data/gmap-2020-11-20+ds/src/atoiindex.c:740:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ptrsfile,"%s.temp",new_pointers_filename);
data/gmap-2020-11-20+ds/src/atoiindex.c:742:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compfile,"%s.temp",new_offsets_filename);
data/gmap-2020-11-20+ds/src/atoiindex.c:911:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ptrsfile,"%s.temp",new_pointers_filename);
data/gmap-2020-11-20+ds/src/atoiindex.c:913:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compfile,"%s.temp",new_offsets_filename);
data/gmap-2020-11-20+ds/src/atoiindex.c:1037:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(destdir,"%s/%s",sourcedir,dbroot);
data/gmap-2020-11-20+ds/src/atoiindex.c:1040:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(destdir,"%s/%s",user_destdir,dbroot);
data/gmap-2020-11-20+ds/src/atoiindex.c:1048:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/atoiindex.c:1080:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pointers_filename,"%s/%s.%s%s",destdir,fileroot,"a2iag",ifilenames->pointers_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1084:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_offsets_filename,"%s/%s.%s%s",destdir,fileroot,"a2iag",ifilenames->offsets_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1088:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_filename,"%s/%s.%s%s",destdir,fileroot,"a2iag",ifilenames->positions_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1093:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_high_filename,"%s/%s.%s%s",destdir,fileroot,"a2iag",ifilenames->positions_high_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1110:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/atoiindex.c:1127:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pointers_filename,"%s/%s.%s%s",destdir,fileroot,"a2itc",ifilenames->pointers_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1131:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_offsets_filename,"%s/%s.%s%s",destdir,fileroot,"a2itc",ifilenames->offsets_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1135:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_filename,"%s/%s.%s%s",destdir,fileroot,"a2itc",ifilenames->positions_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1140:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_high_filename,"%s/%s.%s%s",destdir,fileroot,"a2itc",ifilenames->positions_high_index1info_ptr);
data/gmap-2020-11-20+ds/src/atoiindex.c:1156:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/chrnum.c:30:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(string,label);
data/gmap-2020-11-20+ds/src/chrnum.c:47:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(string[1]),label);
data/gmap-2020-11-20+ds/src/chrom.c:109:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->string,string);
data/gmap-2020-11-20+ds/src/chrom.c:145:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->alpha,p);
data/gmap-2020-11-20+ds/src/cmetindex.c:880:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ptrsfile,"%s.temp",new_pointers_filename);
data/gmap-2020-11-20+ds/src/cmetindex.c:882:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compfile,"%s.temp",new_offsets_filename);
data/gmap-2020-11-20+ds/src/cmetindex.c:1051:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ptrsfile,"%s.temp",new_pointers_filename);
data/gmap-2020-11-20+ds/src/cmetindex.c:1053:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compfile,"%s.temp",new_offsets_filename);
data/gmap-2020-11-20+ds/src/cmetindex.c:1177:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(destdir,"%s/%s",sourcedir,dbroot);
data/gmap-2020-11-20+ds/src/cmetindex.c:1180:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(destdir,"%s/%s",user_destdir,dbroot);
data/gmap-2020-11-20+ds/src/cmetindex.c:1188:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/cmetindex.c:1220:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pointers_filename,"%s/%s.%s%s",destdir,fileroot,"metct",ifilenames->pointers_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1224:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_offsets_filename,"%s/%s.%s%s",destdir,fileroot,"metct",ifilenames->offsets_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1228:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_filename,"%s/%s.%s%s",destdir,fileroot,"metct",ifilenames->positions_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1233:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_high_filename,"%s/%s.%s%s",destdir,fileroot,"metct",ifilenames->positions_high_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1250:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/cmetindex.c:1267:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pointers_filename,"%s/%s.%s%s",destdir,fileroot,"metga",ifilenames->pointers_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1271:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_offsets_filename,"%s/%s.%s%s",destdir,fileroot,"metga",ifilenames->offsets_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1275:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_filename,"%s/%s.%s%s",destdir,fileroot,"metga",ifilenames->positions_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1280:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_high_filename,"%s/%s.%s%s",destdir,fileroot,"metga",ifilenames->positions_high_index1info_ptr);
data/gmap-2020-11-20+ds/src/cmetindex.c:1296:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/datadir.c:55:9: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(line,"%s=%s",seentag,dirbuffer) > 0 && !strcmp(seentag,tag)) {
data/gmap-2020-11-20+ds/src/datadir.c:57:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(directory,dirbuffer);
data/gmap-2020-11-20+ds/src/datadir.c:82:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(configfile,"%s/.gmaprc",p->pw_dir);
data/gmap-2020-11-20+ds/src/datadir.c:190:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(genomedir,user_genomedir);
data/gmap-2020-11-20+ds/src/datadir.c:195:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(genomedir,getenv("GMAPDB"));
data/gmap-2020-11-20+ds/src/datadir.c:207:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(genomedir,GMAPDB);
data/gmap-2020-11-20+ds/src/datadir.c:232:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newgenomedir,"%s/%s",genomedir,dbrootdir);
data/gmap-2020-11-20+ds/src/datadir.c:240:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.version",genomedir,dbroot);
data/gmap-2020-11-20+ds/src/datadir.c:247:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*fileroot,dbroot);
data/gmap-2020-11-20+ds/src/datadir.c:252:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(genomesubdir,"%s/%s",genomedir,dbroot);
data/gmap-2020-11-20+ds/src/datadir.c:269:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.version",genomesubdir,*fileroot);
data/gmap-2020-11-20+ds/src/datadir.c:273:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*dbversion,dbroot);
data/gmap-2020-11-20+ds/src/datadir.c:288:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(mapdir,user_mapdir);
data/gmap-2020-11-20+ds/src/datadir.c:292:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(mapdir,"%s/%s.maps",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/datadir.c:387:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s/%s.version",genomedir,entry->d_name,entry->d_name);
data/gmap-2020-11-20+ds/src/datadir.c:391:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(filename,entry->d_name);
data/gmap-2020-11-20+ds/src/datadir.c:439:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s",mapdir,entry->d_name);
data/gmap-2020-11-20+ds/src/datadir.c:444:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(filename,entry->d_name);
data/gmap-2020-11-20+ds/src/except.c:115:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(piece," %s ", e->reason);
data/gmap-2020-11-20+ds/src/except.c:116:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(message,piece);
data/gmap-2020-11-20+ds/src/except.c:119:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(message,piece);
data/gmap-2020-11-20+ds/src/except.c:122:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(piece," raised at %s:%d",file,line);
data/gmap-2020-11-20+ds/src/except.c:123:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(message,piece);
data/gmap-2020-11-20+ds/src/fopen.c:19:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(command,"%s %s",read_files_command,filename);
data/gmap-2020-11-20+ds/src/fopen.c:22:15: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((fp = popen(command,"r")) == NULL) {
data/gmap-2020-11-20+ds/src/genome-write.c:188:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(accession,&(Header[1]));
data/gmap-2020-11-20+ds/src/genome-write.c:798:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genome",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome-write.c:815:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome-write.c:830:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:185:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/genome.c:189:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:196:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/genome.c:200:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:218:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genome",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:232:47: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Univ_IIT_T chromosome_iit, Access_mode_T access, bool sharedp) {
data/gmap-2020-11-20+ds/src/genome.c:246:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/genome.c:250:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:257:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/genome.c:261:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/genome.c:285:67: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
new->blocks = (Genomecomp_T *) Access_allocate_shared(&new->access,&new->blocks_shmid,&new->blocks_key,
data/gmap-2020-11-20+ds/src/genome.c:288:68: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
new->blocks = (Genomecomp_T *) Access_allocate_private(&new->access,&new->len,&seconds,filename,sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/genome.c:351:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->accession,accession);
data/gmap-2020-11-20+ds/src/genome.h:28:12: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_T access; /* For blocks: ALLOCATED_PRIVATE, ALLOCATED_SHARED, or MMAPPED */
data/gmap-2020-11-20+ds/src/genome.h:57:47: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Univ_IIT_T chromosome_iit, Access_mode_T access, bool sharedp);
data/gmap-2020-11-20+ds/src/get-genome.c:387:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.altstrain.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1017:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dbroot,optarg);
data/gmap-2020-11-20+ds/src/get-genome.c:1064:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.transcripts/%s.align.iit",genomesubdir,fileroot,
data/gmap-2020-11-20+ds/src/get-genome.c:1096:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1109:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(with_colon,"%s:",chr);
data/gmap-2020-11-20+ds/src/get-genome.c:1138:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(iitfile,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1144:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1151:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1176:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1236:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1259:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(with_colon,"%s:",chr);
data/gmap-2020-11-20+ds/src/get-genome.c:1294:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1311:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1318:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.contig.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1340:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1383:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p,string);
data/gmap-2020-11-20+ds/src/get-genome.c:1453:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p,string);
data/gmap-2020-11-20+ds/src/get-genome.c:1472:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1479:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1590:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1597:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1754:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1761:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile);
data/gmap-2020-11-20+ds/src/get-genome.c:1805:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.contig.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/get-genome.c:1819:11: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(line,"%s %s",coords,typestring) < 2) {
data/gmap-2020-11-20+ds/src/gmap.c:5583:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dbroot,optarg);
data/gmap-2020-11-20+ds/src/gmap.c:5837:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(map_iitfile,optarg);
data/gmap-2020-11-20+ds/src/gmap.c:6167:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmap.c:6185:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmap.c:6211:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
data/gmap-2020-11-20+ds/src/gmap.c:6237:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",user_splicingdir,splicing_file);
data/gmap-2020-11-20+ds/src/gmap.c:6250:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",mapdir,splicing_file);
data/gmap-2020-11-20+ds/src/gmap_select.c:51:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:61:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:71:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:81:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:91:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:101:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:111:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmap_select.c:121:12: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:131:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.avx512bw",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:136:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:145:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.avx512",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:150:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.avx2",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:164:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:173:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.sse42",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:178:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:187:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.sse41",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:192:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:201:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.ssse3",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:206:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:215:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.sse2",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:220:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmap_select.c:229:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmap.nosimd",dir);
data/gmap-2020-11-20+ds/src/gmap_select.c:234:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapindex.c:233:8: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(line,"%s %s",strain,straintype) == 2) {
data/gmap-2020-11-20+ds/src/gmapindex.c:241:8: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(refstrain,strain);
data/gmap-2020-11-20+ds/src/gmapindex.c:278:10: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(ptr,"Reference strain: %s",strain) == 1) {
data/gmap-2020-11-20+ds/src/gmapindex.c:284:8: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(refstrain,strain);
data/gmap-2020-11-20+ds/src/gmapindex.c:465:12: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
nitems = sscanf(line,"%s %s %llu",accession_p,chrpos_string,&universal_coord);
data/gmap-2020-11-20+ds/src/gmapindex.c:540:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(typestring,p);
data/gmap-2020-11-20+ds/src/gmapindex.c:610:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(primary_string,"%u..%u,%s:%u..%u\n",
data/gmap-2020-11-20+ds/src/gmapindex.c:616:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(altscaffold_info,primary_string);
data/gmap-2020-11-20+ds/src/gmapindex.c:619:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alt_scaffold_chr,chr_string);
data/gmap-2020-11-20+ds/src/gmapindex.c:630:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(accession,accession_p);
data/gmap-2020-11-20+ds/src/gmapindex.c:722:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(textfile,"%s/%s.chromosome",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:734:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chrsubsetfile,"%s/%s.chrsubset",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:822:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:925:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(string,"%s:%u..%u",primary_chr,primary_start,primary_end);
data/gmap-2020-11-20+ds/src/gmapindex.c:927:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(annot,string);
data/gmap-2020-11-20+ds/src/gmapindex.c:954:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1059:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(textfile,"%s/%s.contig",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1121:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(annot,seglength);
data/gmap-2020-11-20+ds/src/gmapindex.c:1151:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.contig.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1281:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,buffer);
data/gmap-2020-11-20+ds/src/gmapindex.c:1491:11: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(line,"%s %s",chrname,chrname_alt) == 2) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1493:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(key,chrname_alt);
data/gmap-2020-11-20+ds/src/gmapindex.c:1495:22: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
} else if (sscanf(line,"%s",chrname) == 1) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1497:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(key,chrname);
data/gmap-2020-11-20+ds/src/gmapindex.c:1579:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1617:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1627:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.contig.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1667:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(source_genome,argv[i]);
data/gmap-2020-11-20+ds/src/gmapindex.c:1672:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",argv[i],source_dbroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1683:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(inputfiles[i],"%s/%s.genomecomp",argv[i],source_dbroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1693:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outputfile,"%s/%s.genomecomp",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1724:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1752:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1801:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1821:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positionsfile_high,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/gmapindex.c:1828:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positionsfile_low,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/gmapindex.c:1840:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positionsfile_low,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/gmapindex.c:1882:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1912:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(source_genome,argv[i]);
data/gmap-2020-11-20+ds/src/gmapindex.c:1917:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(chromosomefile,"%s/%s.chromosome.iit",argv[i],source_dbroot);
data/gmap-2020-11-20+ds/src/gmapindex.c:1943:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(inputfiles[i],"%s/%s.ref%02d%01dregiondb",
data/gmap-2020-11-20+ds/src/gmapindex.c:1958:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outputfile,"%s/%s.ref%02d%01dregiondb",
data/gmap-2020-11-20+ds/src/gmapl_select.c:51:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:61:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:71:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:81:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:91:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:101:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:111:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gmapl_select.c:121:12: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:131:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.avx512bw",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:136:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:145:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.avx512",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:150:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.avx2",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:164:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:173:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.sse42",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:178:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:187:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.sse41",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:192:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:201:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.ssse3",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:206:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:215:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.sse2",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:220:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gmapl_select.c:229:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gmapl.nosimd",dir);
data/gmap-2020-11-20+ds/src/gmapl_select.c:234:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap.c:2814:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",transcriptomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gsnap.c:2840:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gsnap.c:2858:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/gsnap.c:3013:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",mapdir,snps_root);
data/gmap-2020-11-20+ds/src/gsnap.c:3058:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",mapdir,genes_file);
data/gmap-2020-11-20+ds/src/gsnap.c:3084:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",user_splicingdir,splicing_file);
data/gmap-2020-11-20+ds/src/gsnap.c:3096:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",mapdir,splicing_file);
data/gmap-2020-11-20+ds/src/gsnap.c:3174:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",user_tallydir,tally_root);
data/gmap-2020-11-20+ds/src/gsnap.c:3184:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",genomesubdir,tally_root);
data/gmap-2020-11-20+ds/src/gsnap.c:3212:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",user_runlengthdir,runlength_root);
data/gmap-2020-11-20+ds/src/gsnap.c:3222:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s",genomesubdir,runlength_root);
data/gmap-2020-11-20+ds/src/gsnap_select.c:51:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:61:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:71:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:81:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:91:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:101:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:111:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnap_select.c:121:12: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:131:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.avx512bw",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:136:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:145:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.avx512",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:150:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.avx2",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:164:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:173:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.sse42",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:178:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:187:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.sse41",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:192:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:201:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.ssse3",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:206:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:215:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.sse2",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:220:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnap_select.c:229:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnap.nosimd",dir);
data/gmap-2020-11-20+ds/src/gsnap_select.c:234:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:51:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:61:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:71:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:81:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:91:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:101:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:111:17: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
data/gmap-2020-11-20+ds/src/gsnapl_select.c:121:12: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:131:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.avx512bw",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:136:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:145:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.avx512",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:150:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.avx2",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:164:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:173:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.sse42",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:178:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:187:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.sse41",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:192:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:201:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.ssse3",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:206:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:215:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.sse2",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:220:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:229:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_argv[0],"%s/gsnapl.nosimd",dir);
data/gmap-2020-11-20+ds/src/gsnapl_select.c:234:7: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
rc = execvp(new_argv[0],new_argv);
data/gmap-2020-11-20+ds/src/iit-read-univ.c:118:12: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_T access; /* access type */
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1419:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1546:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read-univ.c:2250:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(string,chrstring);
data/gmap-2020-11-20+ds/src/iit-read.c:114:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read.c:1197:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(strings[type],typestring);
data/gmap-2020-11-20+ds/src/iit-read.c:2557:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read.c:2805:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->name,name);
data/gmap-2020-11-20+ds/src/iit-read.c:3062:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read.c:3082:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->name,name);
data/gmap-2020-11-20+ds/src/iit-read.c:3481:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newfile,"%s.iit",filename);
data/gmap-2020-11-20+ds/src/iit-read.c:6479:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,typestring);
data/gmap-2020-11-20+ds/src/iit-write.c:777:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(new->divstrings[k]),divstring);
data/gmap-2020-11-20+ds/src/iit-write.c:1254:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(new->typestrings[k]),typestring);
data/gmap-2020-11-20+ds/src/iit-write.c:1281:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(new->fieldstrings[k]),fieldstring);
data/gmap-2020-11-20+ds/src/iit-write.c:1314:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(new->labels[k]),label);
data/gmap-2020-11-20+ds/src/iit_get.c:1166:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(nocomment,line);
data/gmap-2020-11-20+ds/src/iit_get.c:1178:20: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if ((nargs = sscanf(nocomment,"%s %s",query,typestring)) == 2) {
data/gmap-2020-11-20+ds/src/iit_store.c:200:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,temp);
data/gmap-2020-11-20+ds/src/iit_store.c:241:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,string);
data/gmap-2020-11-20+ds/src/iit_store.c:296:7: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (sscanf(header,">%s",acc) < 1) {
data/gmap-2020-11-20+ds/src/iit_store.c:302:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*label,acc);
data/gmap-2020-11-20+ds/src/iit_store.c:305:29: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (acc_only_p == true || sscanf(header,">%s %s",acc,query) < 2) {
data/gmap-2020-11-20+ds/src/iit_store.c:308:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(divstring,acc);
data/gmap-2020-11-20+ds/src/iit_store.c:314:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,divstring);
data/gmap-2020-11-20+ds/src/iit_store.c:334:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(divstring,p);
data/gmap-2020-11-20+ds/src/iit_store.c:340:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,divstring);
data/gmap-2020-11-20+ds/src/iit_store.c:380:29: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (acc_only_p == true || sscanf(header,">%s %s %s",acc,query,tag) < 3) {
data/gmap-2020-11-20+ds/src/iit_store.c:399:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*restofheader,p);
data/gmap-2020-11-20+ds/src/iit_store.c:407:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(typestring,tag);
data/gmap-2020-11-20+ds/src/iit_store.c:428:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*restofheader,p);
data/gmap-2020-11-20+ds/src/iit_store.c:452:14: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
nscanned = sscanf(header,">%s %llu %llu",acc,&(*start),&(*end));
data/gmap-2020-11-20+ds/src/iit_store.c:468:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*label,acc);
data/gmap-2020-11-20+ds/src/iit_store.c:497:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(typestring,p);
data/gmap-2020-11-20+ds/src/iit_store.c:522:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(fieldname[1]),line);
data/gmap-2020-11-20+ds/src/iit_store.c:559:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(header[1]),line);
data/gmap-2020-11-20+ds/src/iit_store.c:829:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(labelstr,"%s=",labelid);
data/gmap-2020-11-20+ds/src/iit_store.c:862:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(divstring,"%s",chr);
data/gmap-2020-11-20+ds/src/iit_store.c:891:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(label,Space);
data/gmap-2020-11-20+ds/src/iit_store.c:895:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(label,Space);
data/gmap-2020-11-20+ds/src/iit_store.c:898:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(label,idptr);
data/gmap-2020-11-20+ds/src/iit_store.c:1153:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s.iit",outputfile);
data/gmap-2020-11-20+ds/src/iit_store.c:1159:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(iitfile,outputfile);
data/gmap-2020-11-20+ds/src/iit_store.c:1162:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s.iit",outputfile);
data/gmap-2020-11-20+ds/src/iitdef.h:59:12: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
Access_T access; /* access type */
data/gmap-2020-11-20+ds/src/indexdb-cat.c:699:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(source_genome,argv[genomei]);
data/gmap-2020-11-20+ds/src/indexdb-cat.c:704:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",argv[genomei],source_dbroot);
data/gmap-2020-11-20+ds/src/indexdb-cat.c:733:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(source_genome,argv[genomei]);
data/gmap-2020-11-20+ds/src/indexdb-cat.c:760:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(source_genome,argv[genomei]);
data/gmap-2020-11-20+ds/src/indexdb-cat.c:833:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pages_filename,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-cat.c:841:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_pointers_filename,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-cat.c:848:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_offsets_filename,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-cat.c:856:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_high_filename,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-cat.c:864:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(new_positions_filename,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:764:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:767:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pointersfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:776:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:779:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1140:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pagesfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1143:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pagesfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1152:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1155:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pointersfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1164:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/indexdb-write.c:1167:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/indexdb.c:459:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(locoffsets_suffix,"%s.%s","locoffsets",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:461:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsets_suffix,"%s.%s","offsets",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:463:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_suffix,"%s.%s",POSITIONS_HIGH_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:465:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_suffix,"%s.%s",POSITIONS_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:478:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern,"%s.%s",fileroot,idx_filesuffix);
data/gmap-2020-11-20+ds/src/indexdb.c:552:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/indexdb.c:560:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/indexdb.c:599:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsets_filename,"%s/%s",genomesubdir,base_filename);
data/gmap-2020-11-20+ds/src/indexdb.c:631:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:633:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_high_basename_ptr[rootlength]),positions_high_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:635:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:637:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_basename_ptr[rootlength]),positions_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:763:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetspages_suffix,"offsets32pages.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:764:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsmeta_suffix,"offsets32meta.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:765:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(locoffsetsstrm_suffix,"locoffsets32strm.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:766:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsstrm_suffix,"offsets32strm.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:767:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_suffix,"%s.%s",POSITIONS_HIGH_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:768:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_suffix,"%s.%s",POSITIONS_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:778:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetspages_suffix,"offsets64pages.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:779:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsmeta_suffix,"offsets64meta.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:780:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(locoffsetsstrm_suffix,"locoffsets64strm.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:781:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsstrm_suffix,"offsets64strm.%s",snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:782:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_suffix,"%s.%s",POSITIONS_HIGH_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:783:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_suffix,"%s.%s",POSITIONS_FILESUFFIX,snps_root);
data/gmap-2020-11-20+ds/src/indexdb.c:808:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern1,"%s.",fileroot);
data/gmap-2020-11-20+ds/src/indexdb.c:812:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern2,".%s",idx_filesuffix);
data/gmap-2020-11-20+ds/src/indexdb.c:886:8: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/indexdb.c:900:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern,"%s.%s",fileroot,idx_filesuffix);
data/gmap-2020-11-20+ds/src/indexdb.c:953:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/indexdb.c:990:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsstrm_filename,"%s/%s",genomesubdir,base_filename);
data/gmap-2020-11-20+ds/src/indexdb.c:1020:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsmeta_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1022:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(offsetsmeta_basename_ptr[rootlength]),offsetsmeta_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:1044:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetspages_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1046:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(offsetspages_basename_ptr[rootlength]),offsetspages_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:1061:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1063:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_high_basename_ptr[rootlength]),positions_high_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:1065:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1067:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_basename_ptr[rootlength]),positions_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:1073:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_high_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1076:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_high_basename_ptr[rootlength]),positions_high_suffix);
data/gmap-2020-11-20+ds/src/indexdb.c:1078:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(positions_filename,"%s/",genomesubdir);
data/gmap-2020-11-20+ds/src/indexdb.c:1081:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(&(positions_basename_ptr[rootlength]),positions_suffix);
data/gmap-2020-11-20+ds/src/intlist.c:454:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/intlist.c:457:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/outbuffer.c:171:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.1",failedinput_root);
data/gmap-2020-11-20+ds/src/outbuffer.c:179:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.2",failedinput_root);
data/gmap-2020-11-20+ds/src/outbuffer.c:186:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s",failedinput_root);
data/gmap-2020-11-20+ds/src/outbuffer.c:196:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s",failedinput_root);
data/gmap-2020-11-20+ds/src/pair.c:759:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (this->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:788:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(Buffer,"%s:%llu",chrstring, (unsigned long long) (this->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:817:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (start->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:824:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (end->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:2398:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new_token,old_token);
data/gmap-2020-11-20+ds/src/pair.c:2437:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,token);
data/gmap-2020-11-20+ds/src/parserange.c:82:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,string);
data/gmap-2020-11-20+ds/src/parserange.c:256:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/parserange.c:407:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/parserange.c:452:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/parserange.c:507:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/parserange.c:524:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/regiondb-write.c:151:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(regionfile,"%s/%s.%s.%s%d%c%s",
data/gmap-2020-11-20+ds/src/regiondb-write.c:154:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(regionfile,"%s/%s.%s%02d%c%s",
data/gmap-2020-11-20+ds/src/regiondb.c:1516:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(regiondb_suffix,"regiondb.%s",snps_root);
data/gmap-2020-11-20+ds/src/regiondb.c:1534:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern1,"%s.",fileroot);
data/gmap-2020-11-20+ds/src/regiondb.c:1538:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern2,".%s",idx_filesuffix);
data/gmap-2020-11-20+ds/src/regiondb.c:1605:8: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/regiondb.c:1619:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pattern,"%s.%s",fileroot,idx_filesuffix);
data/gmap-2020-11-20+ds/src/regiondb.c:1664:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(base_filename,filename);
data/gmap-2020-11-20+ds/src/regiondb.c:1696:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(regiondb_filename,"%s/%s",genomesubdir,base_filename);
data/gmap-2020-11-20+ds/src/sam_sort.c:921:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ptr,p);
data/gmap-2020-11-20+ds/src/sam_sort.c:1956:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dbroot,optarg);
data/gmap-2020-11-20+ds/src/sam_sort.c:1977:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
data/gmap-2020-11-20+ds/src/samheader.c:30:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s",split_output_root);
data/gmap-2020-11-20+ds/src/samheader.c:86:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.%s",split_output_root,suffix);
data/gmap-2020-11-20+ds/src/samread.c:1195:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p,newflag_string);
data/gmap-2020-11-20+ds/src/samread.c:1200:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p,line);
data/gmap-2020-11-20+ds/src/sequence.c:125:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(header,"Annot=\"%s\"",p);
data/gmap-2020-11-20+ds/src/sequence.c:604:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(this->acc,Header);
data/gmap-2020-11-20+ds/src/sequence.c:611:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(this->acc,Header);
data/gmap-2020-11-20+ds/src/sequence.c:614:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(this->restofheader,p);
data/gmap-2020-11-20+ds/src/sequence.c:1230:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->quality,this->quality);
data/gmap-2020-11-20+ds/src/shortread.c:411:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:418:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:421:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*restofheader,p);
data/gmap-2020-11-20+ds/src/shortread.c:484:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:491:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:494:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*restofheader,p);
data/gmap-2020-11-20+ds/src/shortread.c:558:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:565:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,Header);
data/gmap-2020-11-20+ds/src/shortread.c:568:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*restofheader,p);
data/gmap-2020-11-20+ds/src/shortread.c:730:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,start);
data/gmap-2020-11-20+ds/src/shortread.c:816:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,start);
data/gmap-2020-11-20+ds/src/shortread.c:903:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(acc,start);
data/gmap-2020-11-20+ds/src/shortread.c:2149:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->acc,acc);
data/gmap-2020-11-20+ds/src/shortread.c:2158:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->restofheader,restofheader);
data/gmap-2020-11-20+ds/src/simplepair.c:382:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(copy,token);
data/gmap-2020-11-20+ds/src/snpindex.c:1301:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.iit",mapdir,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1323:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.chromosome.iit",sourcedir,fileroot);
data/gmap-2020-11-20+ds/src/snpindex.c:1382:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(snp_offsetsmetafile,"%s/%s.%s",destdir,indexdb_filenames->pointers_basename_ptr,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1385:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(snp_offsetsstrmfile,"%s/%s.%s",destdir,indexdb_filenames->offsets_basename_ptr,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1388:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(snponly_offsetsmetafile,"%s.only",snp_offsetsmetafile);
data/gmap-2020-11-20+ds/src/snpindex.c:1390:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(snponly_offsetsstrmfile,"%s.only",snp_offsetsstrmfile);
data/gmap-2020-11-20+ds/src/snpindex.c:1402:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomecomp.%s",destdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1423:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.genomebits128.%s",destdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1502:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.%s",destdir,indexdb_filenames->positions_high_basename_ptr,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1512:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.%s",destdir,indexdb_filenames->positions_basename_ptr,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1616:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename1,"%s/%s.iit",mapdir,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1628:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.maps/%s.iit",destdir,fileroot,snps_root);
data/gmap-2020-11-20+ds/src/snpindex.c:1632:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s/%s.iit",destdir,snps_root);
data/gmap-2020-11-20+ds/src/substring.c:3770:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->genomic_bothdiff,old->genomic_bothdiff);
data/gmap-2020-11-20+ds/src/substring.c:3777:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->genomic_bothdiff,old->genomic_bothdiff);
data/gmap-2020-11-20+ds/src/substring.c:3779:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new->genomic_refdiff,old->genomic_refdiff);
data/gmap-2020-11-20+ds/src/transcriptome.c:117:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(info_root,"%s/%s.transcripts/%s",genomesubdir,genome_fileroot,transcriptome_fileroot);
data/gmap-2020-11-20+ds/src/transcriptome.c:120:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.chrnums",info_root);
data/gmap-2020-11-20+ds/src/transcriptome.c:139:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.offsets64meta",info_root);
data/gmap-2020-11-20+ds/src/transcriptome.c:156:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.offsets64strm",info_root);
data/gmap-2020-11-20+ds/src/transcriptome.c:174:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.exoninfo",info_root);
data/gmap-2020-11-20+ds/src/trindex.c:179:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(info_root,"%s/%s.transcripts/%s",genomesubdir,genome_fileroot,transcriptome_fileroot);
data/gmap-2020-11-20+ds/src/trindex.c:198:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.align.iit",info_root);
data/gmap-2020-11-20+ds/src/trindex.c:218:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,genome_fileroot);
data/gmap-2020-11-20+ds/src/trindex.c:228:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(iitfile,"%s/%s.chromosome.iit",transcriptomesubdir,transcriptome_fileroot);
data/gmap-2020-11-20+ds/src/trindex.c:245:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.exoninfo",info_root);
data/gmap-2020-11-20+ds/src/trindex.c:284:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s.chrnums",info_root);
data/gmap-2020-11-20+ds/src/trindex.c:295:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(pointersfile,"%s.offsets64meta",info_root);
data/gmap-2020-11-20+ds/src/trindex.c:298:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(offsetsfile,"%s.offsets64strm",info_root);
data/gmap-2020-11-20+ds/src/uint8list.c:292:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:295:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:324:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:327:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:293:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:296:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:325:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:328:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(string,Buffer);
data/gmap-2020-11-20+ds/src/atoiindex.c:991:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"F:D:d:k:q:v:",
data/gmap-2020-11-20+ds/src/cmetindex.c:1131:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"F:D:d:k:q:v:",
data/gmap-2020-11-20+ds/src/datadir.c:79:15: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((user = getenv("USER")) != NULL) {
data/gmap-2020-11-20+ds/src/datadir.c:192:14: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
} else if (getenv("GMAPDB") != NULL) {
data/gmap-2020-11-20+ds/src/datadir.c:194:40: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
genomedir = (char *) CALLOC(strlen(getenv("GMAPDB"))+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:195:22: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
strcpy(genomedir,getenv("GMAPDB"));
data/gmap-2020-11-20+ds/src/get-genome.c:961:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"D:d:c:CUl:h:V:v:f:M:m:kru:ESALI^?",
data/gmap-2020-11-20+ds/src/gmap.c:5245:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,
data/gmap-2020-11-20+ds/src/gmapindex.c:1321:5: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int getopt (int argc, char *const argv[], const char *optstring);
data/gmap-2020-11-20+ds/src/gmapindex.c:1362:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc,argv,"D:d:z:k:q:j:ArlGZCUNHOPQRWw:e:Ss:n:m9")) != -1) {
data/gmap-2020-11-20+ds/src/gsnap.c:1707:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,
data/gmap-2020-11-20+ds/src/iit_dump.c:201:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"9STCIA",long_options,&long_option_index)) != -1) {
data/gmap-2020-11-20+ds/src/iit_get.c:164:5: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int getopt (int argc, char *const argv[], const char *optstring);
data/gmap-2020-11-20+ds/src/iit_get.c:986:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"a:b:f:LCASUu:c:HRTZN",long_options,&long_option_index)) != -1) {
data/gmap-2020-11-20+ds/src/iit_store.c:929:5: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int getopt (int argc, char *const argv[], const char *optstring);
data/gmap-2020-11-20+ds/src/iit_store.c:956:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"o:1FGl:v:s:",
data/gmap-2020-11-20+ds/src/indexdb-cat.c:647:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"F:D:d:k:q:v:",
data/gmap-2020-11-20+ds/src/sam_sort.c:1882:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"D:d:^?",
data/gmap-2020-11-20+ds/src/snpindex.c:1239:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"D:d:k:q:V:v:w:",
data/gmap-2020-11-20+ds/src/trindex.c:129:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((opt = getopt_long(argc,argv,"D:d:c:",
data/gmap-2020-11-20+ds/src/access.c:193:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fd = open(filename,O_RDONLY,0764)) < 0) {
data/gmap-2020-11-20+ds/src/access.c:204:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fd = open(filename,O_RDWR | O_CREAT | O_TRUNC,0764)) < 0) {
data/gmap-2020-11-20+ds/src/access.c:531:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
p = (void *) &(((unsigned char *) memory)[i]);
data/gmap-2020-11-20+ds/src/access.c:536:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
p = (void *) &(((unsigned char *) memory)[i]);
data/gmap-2020-11-20+ds/src/access.c:594:31: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
p = (void *) &(((unsigned char *) memory)[0]);
data/gmap-2020-11-20+ds/src/access.c:829:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if (((unsigned char *) memory)[i] != ((unsigned char *) memory2)[i]) {
data/gmap-2020-11-20+ds/src/access.c:829:53: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if (((unsigned char *) memory)[i] != ((unsigned char *) memory2)[i]) {
data/gmap-2020-11-20+ds/src/access.c:916:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if (((unsigned char *) memory)[i] != ((unsigned char *) memory2)[i]) {
data/gmap-2020-11-20+ds/src/access.c:916:53: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if (((unsigned char *) memory)[i] != ((unsigned char *) memory2)[i]) {
data/gmap-2020-11-20+ds/src/access.c:987:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
*fd = open(filename,O_RDONLY,0764); /* Still need to initialize value */
data/gmap-2020-11-20+ds/src/access.c:990:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((*fd = open(filename,O_RDONLY,0764)) < 0) {
data/gmap-2020-11-20+ds/src/access.c:1134:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
*fd = open(filename,O_RDWR,0764); /* Still need to initialize value */
data/gmap-2020-11-20+ds/src/access.c:1136:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((*fd = open(filename,O_RDWR,0764)) < 0) {
data/gmap-2020-11-20+ds/src/access.c:1285:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
*fd = open(filename,O_RDONLY,0764); /* Still need to initialize value */
data/gmap-2020-11-20+ds/src/access.c:1288:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((*fd = open(filename,O_RDONLY,0764)) < 0) {
data/gmap-2020-11-20+ds/src/access.c:1338:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if (((char *) memory)[i] == 0) {
data/gmap-2020-11-20+ds/src/atoiindex.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/atoiindex.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/atoiindex.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/atoiindex.c:1013:37: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': required_index1part = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/atoiindex.c:1014:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': required_index1interval = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/atoiindex.c:1111:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((sequence_fp = fopen(filename,"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/atoiindex.c:1157:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((sequence_fp = fopen(filename,"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/bigendian.c:13:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[1];
data/gmap-2020-11-20+ds/src/bigendian.c:28:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[2];
data/gmap-2020-11-20+ds/src/bigendian.c:42:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:82:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:99:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:119:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:143:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:192:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:209:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:222:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:243:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:267:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:297:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/bigendian.c:357:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:374:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:395:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:420:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:448:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:482:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/bigendian.c:512:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8], *ptr = (unsigned char *) &value;
data/gmap-2020-11-20+ds/src/bzip2.c:46:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(filename,"r");
data/gmap-2020-11-20+ds/src/bzip2.c:149:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char string[100];
data/gmap-2020-11-20+ds/src/chrom.c:143:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
new->num = atoi(string);
data/gmap-2020-11-20+ds/src/chrom.c:174:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
new->num = atoi(p);
data/gmap-2020-11-20+ds/src/cigar.c:571:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/cmetindex.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/cmetindex.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/cmetindex.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/cmetindex.c:1153:37: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': required_index1part = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/cmetindex.c:1154:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': required_index1interval = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/cmetindex.c:1251:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((sequence_fp = fopen(filename,"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/cmetindex.c:1297:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((sequence_fp = fopen(filename,"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/compress-write.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress-write.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress-write.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress-write.c:46:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/compress-write.c:200:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char section[15];
data/gmap-2020-11-20+ds/src/compress-write.c:339:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char acgt[4] = {'A','C','G','T'};
data/gmap-2020-11-20+ds/src/compress-write.c:340:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char non_acgt[4] = {'N','?','?','X'};
data/gmap-2020-11-20+ds/src/compress-write.c:351:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/compress-write.c:442:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/compress-write.c:549:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen(files[filei],"r")) == NULL) {
data/gmap-2020-11-20+ds/src/compress-write.c:861:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen((file = *files++),"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/compress-write.c:906:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen((file = *files++),"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/compress.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/compress.c:145:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/compress.c:442:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(new->shift_array[0]),new->blocks,new->nblocks*COMPRESS_BLOCKSIZE*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/compress.c:571:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(new->shift_array[0]),new->blocks,new->nblocks*COMPRESS_BLOCKSIZE*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/compress.c:894:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(shifted[ptr]),&(this->blocks[ptr]),12*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/compress.c:1324:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(shifted[ptr]),&(this->blocks[ptr]),12*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/compress.c:1635:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(shifted[ptr]),&(this->blocks[ptr]),COMPRESS_BLOCKSIZE*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/distant-dna.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/distant-dna.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/distant-dna.c:9:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/distant-rna.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/distant-rna.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/distant-rna.c:9:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/dynprog.c:140:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog.c:1188:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, Score32_T open, Score32_T extend,
data/gmap-2020-11-20+ds/src/dynprog.c:1207:87: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_standard. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog.c:1234:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
penalty = open;
data/gmap-2020-11-20+ds/src/dynprog.c:1247:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
penalty = open;
data/gmap-2020-11-20+ds/src/dynprog.c:1275:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
penalty = open;
data/gmap-2020-11-20+ds/src/dynprog.c:1294:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
penalty = open;
data/gmap-2020-11-20+ds/src/dynprog.c:1303:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
penalty = open;
data/gmap-2020-11-20+ds/src/dynprog.c:1380:38: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
bestscore = matrix3[c][r-1].nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog.c:1401:70: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (lowerp == true && c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog.c:1412:38: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
bestscore = matrix3[c-1][r].nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog.c:1433:71: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (upperp == true && r_gap[r] /* + extend */ >= (score = nogap[r] + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog.c:1567:38: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
bestscore = matrix3[c][r-1].nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog.c:1588:69: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (lowerp == true && c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog.c:1599:38: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
bestscore = matrix3[c-1][r].nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog.c:1620:70: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (upperp == true && r_gap[r] /* + extend */ > (score = nogap[r] + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog.h:255:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, Score32_T open, Score32_T extend,
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:68:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:129:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, int extend, int leftoffset, int rightoffset, bool jump_late_p) {
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:393:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, int extend, int leftoffset, int rightoffset, bool jump_late_p) {
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:661:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, int extend, int leftoffset, int rightoffset, bool jump_late_p) {
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:806:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:951:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:958:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:968:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:976:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:983:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,roffsetL,rev_roffsetR,jump_late_p);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1081:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1088:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1097:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1105:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1112:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,roffsetL,rev_roffsetR,jump_late_p);
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1209:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,ubandL,
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1217:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,ubandR,
data/gmap-2020-11-20+ds/src/dynprog_cdna.c:1225:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,roffsetL,rev_roffsetR,jump_late_p);
data/gmap-2020-11-20+ds/src/dynprog_end.c:589:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog_end.c:1277:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_end.c:1389:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1397:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1410:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1418:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1430:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lband,uband,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1452:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1460:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1473:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1481:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1493:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lband,uband,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1631:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_end.c:1714:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1722:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1735:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1743:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1754:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lband,uband,
data/gmap-2020-11-20+ds/src/dynprog_end.c:1865:64: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
*finalscore,FULLMATCH,*nmatches,MISMATCH_ENDQ,*nmismatches,open,*nopens,extend,*nindels));
data/gmap-2020-11-20+ds/src/dynprog_end.c:1899:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_end.c:1997:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2004:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2015:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2022:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2032:66: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
genome,genomealt,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2051:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2058:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2070:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2077:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2088:66: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
genome,genomealt,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2219:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_end.c:2305:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2312:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2325:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2332:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2343:64: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
genome,genomealt,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_end.c:2436:64: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
*finalscore,FULLMATCH,*nmatches,MISMATCH_ENDQ,*nmismatches,open,*nopens,extend,*nindels));
data/gmap-2020-11-20+ds/src/dynprog_genome.c:216:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3290:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3497:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3505:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3516:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3525:21: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3634:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3642:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3652:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3661:23: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3770:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,ubandL,
data/gmap-2020-11-20+ds/src/dynprog_genome.c:3779:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,lbandL,ubandR,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2290:37: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2310:85: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2312:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
jump_late_p,open,extend,lband,uband));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2452:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2475:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _mm_set1_epi8(NEG_INFINITY_8-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2488:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2493:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2502:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2646:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2660:54: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2701:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _mm_set1_epi8(NEG_INFINITY_8-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2714:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2729:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2872:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2886:53: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:2966:36: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3013:85: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3015:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
jump_late_p,open,extend,lband,uband));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3155:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3185:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3198:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3203:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3212:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3397:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3411:54: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3456:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3469:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3484:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3670:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3684:53: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3748:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,uband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3753:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3795:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3815:91: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3816:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3918:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:3939:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4063:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4240:42: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4280:91: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4281:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4383:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4404:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4566:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4742:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,uband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4748:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,/*lband*/0,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4788:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4807:91: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4808:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4950:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:4969:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5089:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5240:42: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5279:91: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5280:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5422:39: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI8((Score8_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5442:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5599:48: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5769:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5774:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,/*uband*/0,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5815:38: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5832:86: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5834:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
jump_late_p,open,extend,lband,uband));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5949:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5972:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _mm_set1_epi16(NEG_INFINITY_16-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5985:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:5990:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6000:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6124:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6138:54: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6179:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _mm_set1_epi16(NEG_INFINITY_16-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6192:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6208:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6329:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6343:53: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6423:37: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6469:86: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6471:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
jump_late_p,open,extend,lband,uband));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6586:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6613:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6626:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6631:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6641:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6809:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6823:54: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6868:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16-open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6881:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:6897:45: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7062:25: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
score = last_nogap + open /* + extend */;
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7076:53: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7140:12: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,uband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7145:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7188:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7202:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7203:93: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7297:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7313:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7408:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7533:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7565:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7566:93: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7660:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7677:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7810:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7953:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,uband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:7959:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,/*lband*/0,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8000:44: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8013:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8014:93: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8140:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _mm_set1_epi16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8155:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8246:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8369:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8401:92: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug2(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8402:93: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
debug15(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8528:41: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
gap_open = _MM_SET1_EPI16((Score16_T) open);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8544:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8673:50: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
H_nogap_c = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8816:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,jump_late_p,revp);
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8822:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open,extend,lband,/*uband*/0,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
data/gmap-2020-11-20+ds/src/dynprog_simd.c:8857:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog_simd.h:24:36: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.h:34:42: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.h:44:42: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.h:55:37: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.h:65:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_simd.h:75:43: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Mismatchtype_T mismatchtype, int open, int extend,
data/gmap-2020-11-20+ds/src/dynprog_single.c:112:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/dynprog_single.c:438:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int open, extend;
data/gmap-2020-11-20+ds/src/dynprog_single.c:594:22: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_single.c:611:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/dynprog_single.c:627:64: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
genome,genomealt,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
data/gmap-2020-11-20+ds/src/except.c:107:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char message[512], piece[128];
data/gmap-2020-11-20+ds/src/except.c:118:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(piece," at 0x%p",(void *) e);
data/gmap-2020-11-20+ds/src/extension-search.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/extension-search.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/extension-search.c:112:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char conversion_fwd[128];
data/gmap-2020-11-20+ds/src/extension-search.c:113:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char conversion_rev[128];
data/gmap-2020-11-20+ds/src/filestring.c:299:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/filestring.c:356:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char BUFFER[BUFFERLEN];
data/gmap-2020-11-20+ds/src/filestring.c:388:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%p",va_arg(values, void *));
data/gmap-2020-11-20+ds/src/filestring.c:417:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%.*f",precision,va_arg(values, double));
data/gmap-2020-11-20+ds/src/filestring.c:422:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%.*e",precision,va_arg(values, double));
data/gmap-2020-11-20+ds/src/filestring.c:427:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%.*g",precision,va_arg(values, double));
data/gmap-2020-11-20+ds/src/filestring.c:452:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%*d",precision,va_arg(values, int));
data/gmap-2020-11-20+ds/src/filestring.c:456:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%*u",precision,va_arg(values, unsigned int));
data/gmap-2020-11-20+ds/src/filestring.c:498:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%d",va_arg(values, int));
data/gmap-2020-11-20+ds/src/filestring.c:503:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%f",va_arg(values, double));
data/gmap-2020-11-20+ds/src/filestring.c:508:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%u",va_arg(values, unsigned int));
data/gmap-2020-11-20+ds/src/filestring.c:515:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%ld",va_arg(values, long int));
data/gmap-2020-11-20+ds/src/filestring.c:520:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%lu",va_arg(values, unsigned long));
data/gmap-2020-11-20+ds/src/filestring.c:527:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%lld",va_arg(values, long long int));
data/gmap-2020-11-20+ds/src/filestring.c:532:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(BUFFER,"%llu",va_arg(values, unsigned long long));
data/gmap-2020-11-20+ds/src/fopen.c:29:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename,"rt")) == NULL) {
data/gmap-2020-11-20+ds/src/fopen.c:33:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename,"r")) == NULL) {
data/gmap-2020-11-20+ds/src/fopen.h:11:37: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_READ_BINARY(filename) fopen(filename,"rb")
data/gmap-2020-11-20+ds/src/fopen.h:12:38: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_WRITE_BINARY(filename) fopen(filename,"wb")
data/gmap-2020-11-20+ds/src/fopen.h:13:35: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_RW_BINARY(filename) fopen(filename,"w+b")
data/gmap-2020-11-20+ds/src/fopen.h:15:37: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_READ_BINARY(filename) fopen(filename,"r")
data/gmap-2020-11-20+ds/src/fopen.h:16:38: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_WRITE_BINARY(filename) fopen(filename,"w")
data/gmap-2020-11-20+ds/src/fopen.h:17:35: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_RW_BINARY(filename) fopen(filename,"w+")
data/gmap-2020-11-20+ds/src/fopen.h:21:35: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_READ_TEXT(filename) fopen(filename,"rt")
data/gmap-2020-11-20+ds/src/fopen.h:22:36: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_WRITE_TEXT(filename) fopen(filename,"wt")
data/gmap-2020-11-20+ds/src/fopen.h:23:33: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_RW_TEXT(filename) fopen(filename,"w+t")
data/gmap-2020-11-20+ds/src/fopen.h:25:35: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_READ_TEXT(filename) fopen(filename,"r")
data/gmap-2020-11-20+ds/src/fopen.h:26:36: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_WRITE_TEXT(filename) fopen(filename,"w")
data/gmap-2020-11-20+ds/src/fopen.h:27:33: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
#define FOPEN_RW_TEXT(filename) fopen(filename,"w+")
data/gmap-2020-11-20+ds/src/genome-write.c:122:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Empty[WRITEBLOCK];
data/gmap-2020-11-20+ds/src/genome-write.c:207:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/genome-write.c:224:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[BUFFERSIZE], Complement[BUFFERSIZE], *segment;
data/gmap-2020-11-20+ds/src/genome-write.c:401:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[BUFFERSIZE], Reverse[BUFFERSIZE], *segment;
data/gmap-2020-11-20+ds/src/genome-write.c:625:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[BUFFERSIZE], Complement[BUFFERSIZE], *segment;
data/gmap-2020-11-20+ds/src/genome.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome.c:360:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/genome.c:402:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4];
data/gmap-2020-11-20+ds/src/genome.c:419:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char DEFAULT_CHARS[4] = {'A','C','G','T'};
data/gmap-2020-11-20+ds/src/genome.c:420:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char DEFAULT_FLAGS[4] = {'N','N','N','N'};
data/gmap-2020-11-20+ds/src/genome.c:421:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char X_FLAGS[4] = {'X','X','X','X'};
data/gmap-2020-11-20+ds/src/genome.c:423:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char A_FLAGS[4] = {'A','A','A','A'};
data/gmap-2020-11-20+ds/src/genome.c:427:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char SNP_CHARS[4] = {' ',' ',' ',' '};
data/gmap-2020-11-20+ds/src/genome.c:429:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char SNP_FLAGS[4] = {'A','C','G','T'};
data/gmap-2020-11-20+ds/src/genome.c:445:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char *nucleotides[65536] =
data/gmap-2020-11-20+ds/src/genome.c:8649:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:8752:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32], c;
data/gmap-2020-11-20+ds/src/genome.c:8881:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:8998:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:9019:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9020:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9021:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9022:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9031:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard));
data/gmap-2020-11-20+ds/src/genome.c:9042:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9043:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9044:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9045:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9054:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard);
data/gmap-2020-11-20+ds/src/genome.c:9066:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[low & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9067:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[low >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9068:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[high & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9069:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[high >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9090:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9091:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9092:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9093:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9102:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),Buffer,enddiscard);
data/gmap-2020-11-20+ds/src/genome.c:9117:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:9138:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9139:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9140:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9141:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9150:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard));
data/gmap-2020-11-20+ds/src/genome.c:9161:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9162:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9163:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9164:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9173:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard);
data/gmap-2020-11-20+ds/src/genome.c:9185:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[low & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9186:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[low >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9187:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[high & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9188:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[high >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9209:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[low & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9210:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[low >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9211:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[high & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9212:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[high >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9221:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),Buffer,enddiscard);
data/gmap-2020-11-20+ds/src/genome.c:9241:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:9261:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9262:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9263:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9264:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9282:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard));
data/gmap-2020-11-20+ds/src/genome.c:9293:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9294:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9295:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9296:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9314:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard);
data/gmap-2020-11-20+ds/src/genome.c:9326:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[altlow & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9327:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[altlow >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9328:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[althigh & 0x0000FFFF],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9329:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),nucleotides[althigh >> 16],8); k += 8;
data/gmap-2020-11-20+ds/src/genome.c:9360:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,nucleotides[altlow & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9361:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[8]),nucleotides[altlow >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9362:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[16]),nucleotides[althigh & 0x0000FFFF],8);
data/gmap-2020-11-20+ds/src/genome.c:9363:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(Buffer[24]),nucleotides[althigh >> 16],8);
data/gmap-2020-11-20+ds/src/genome.c:9381:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),Buffer,enddiscard);
data/gmap-2020-11-20+ds/src/genome.c:9392:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char EMPTY_32[32] = " ";
data/gmap-2020-11-20+ds/src/genome.c:9400:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32];
data/gmap-2020-11-20+ds/src/genome.c:9421:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,EMPTY_32,32);
data/gmap-2020-11-20+ds/src/genome.c:9438:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),(enddiscard - startdiscard));
data/gmap-2020-11-20+ds/src/genome.c:9449:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,EMPTY_32,32);
data/gmap-2020-11-20+ds/src/genome.c:9466:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer1,&(Buffer[startdiscard]),k = 32 - startdiscard);
data/gmap-2020-11-20+ds/src/genome.c:9478:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),EMPTY_32,32);
data/gmap-2020-11-20+ds/src/genome.c:9509:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(Buffer,EMPTY_32,32);
data/gmap-2020-11-20+ds/src/genome.c:9526:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(gbuffer1[k]),Buffer,enddiscard);
data/gmap-2020-11-20+ds/src/genome.c:9578:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char CHARTABLE[4] = {'A','C','G','T'};
data/gmap-2020-11-20+ds/src/genome.c:9620:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[32], c;
data/gmap-2020-11-20+ds/src/genome.c:9777:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer_debug[1024];
data/gmap-2020-11-20+ds/src/genome128_consec.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_consec.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_consec.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_consec.c:244:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/genome128_hr.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_hr.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_hr.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome128_hr.c:239:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/genome_canonical.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_canonical.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_canonical.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_sites.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_sites.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_sites.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genome_sites.c:44:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/genomicpos.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genomicpos.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genomicpos.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/genomicpos.c:58:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(string,ptr,len+1);
data/gmap-2020-11-20+ds/src/genomicpos.c:98:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(string,ptr,len+1);
data/gmap-2020-11-20+ds/src/get-genome.c:549:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/get-genome.c:1023:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'l': wraplength = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/get-genome.c:1027:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'f': print_snps_mode = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/get-genome.c:1033:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'u': nflanking = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/get-genome.c:1362:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(argv[i],"r")) == NULL) {
data/gmap-2020-11-20+ds/src/getline.c:40:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer,ptr,length*sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:77:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer,ptr,length*sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:114:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer,ptr,length*sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:152:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer,ptr,length*sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:191:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer,ptr,length*sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:218:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(argv[1],"r");
data/gmap-2020-11-20+ds/src/gmap.c:4708:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acc[100+1], comma0[20], comma1[20], comma2[20], comma3[20], comma4[20], comma5[20];
data/gmap-2020-11-20+ds/src/gmap.c:4856:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char threadname[12];
data/gmap-2020-11-20+ds/src/gmap.c:4857:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acc[100+1], comma0[20], comma1[20], comma2[20], comma3[20], comma4[20], comma5[20];
data/gmap-2020-11-20+ds/src/gmap.c:4858:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(threadname,"thread-%ld",worker_id);
data/gmap-2020-11-20+ds/src/gmap.c:5288:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
required_index1interval = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5314:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
translation_code = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5320:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
max_deletionlength = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5323:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
min_intronlength = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5326:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
maxintronlen = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5329:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
maxintronlen_ends = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5335:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
minendexon = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5357:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
suboptimal_score_start = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5359:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
suboptimal_score_end = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5379:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
user_open = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5391:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
user_extend = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5445:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
inbuffer_nspaces = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5447:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
output_buffer_size = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5591:37: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': required_index1part = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5594:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
required_index1part = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5670:50: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'K': maxintronlen = maxintronlen_ends = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5674:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'L': maxtotallen_bound = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5677:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
chimera_margin = atoi(check_valid_int(optarg))/3;
data/gmap-2020-11-20+ds/src/gmap.c:5679:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
chimera_margin = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5693:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 't': nworkers = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5702:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'p': switch (atoi(check_valid_int(optarg))) {
data/gmap-2020-11-20+ds/src/gmap.c:5760:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
maxpaths_report = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5829:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'o': chimera_overlap = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5845:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'u': nflanking = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5869:30: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'a': cds_startpos = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5898:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
quality_shift = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gmap.c:5905:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'I': invertmode = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5906:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'i': user_ngap = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmap.c:5907:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'l': wraplength = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gmapindex.c:223:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(strainfile,"r");
data/gmap-2020-11-20+ds/src/gmapindex.c:258:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(refstrain,"reference");
data/gmap-2020-11-20+ds/src/gmapindex.c:270:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(coordsfile,"r");
data/gmap-2020-11-20+ds/src/gmapindex.c:300:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(refstrain,"reference");
data/gmap-2020-11-20+ds/src/gmapindex.c:383:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[BUFFERSIZE], *p;
data/gmap-2020-11-20+ds/src/gmapindex.c:413:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[BUFFERSIZE];
data/gmap-2020-11-20+ds/src/gmapindex.c:676:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *divstring, *textfile, *chrsubsetfile, *iitfile, *chr_string, emptystring[1];
data/gmap-2020-11-20+ds/src/gmapindex.c:1019:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char **accessions, *divstring, seglength[12]; /* 2^32 = 4*10^9 */
data/gmap-2020-11-20+ds/src/gmapindex.c:1109:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(seglength,"-%u",Segmentpos_length(segmentpos));
data/gmap-2020-11-20+ds/src/gmapindex.c:1117:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(seglength,"%u",Segmentpos_length(segmentpos));
data/gmap-2020-11-20+ds/src/gmapindex.c:1234:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
accession = (char *) keys[i];
data/gmap-2020-11-20+ds/src/gmapindex.c:1259:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
altloc_chr = (char *) keys[i];
data/gmap-2020-11-20+ds/src/gmapindex.c:1263:27: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
altscaffold_info = (char *) values[i];
data/gmap-2020-11-20+ds/src/gmapindex.c:1376:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': index1part = atoi(optarg);
data/gmap-2020-11-20+ds/src/gmapindex.c:1382:32: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': index1interval = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/gmapindex.c:1384:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'j': region1part = atoi(optarg);
data/gmap-2020-11-20+ds/src/gmapindex.c:1410:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'w': wraplength = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/gmapindex.c:1411:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'e': nmessages = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/gmapindex.c:1482:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen(sortfilename,"r")) == NULL) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1670:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1681:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1745:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen(argv[0],"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1794:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen(argv[0],"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1875:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen(argv[0],"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/gmapindex.c:1915:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1941:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:221:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char STANDARD_CHARTABLE[4] = {'A','C','G','T'};
data/gmap-2020-11-20+ds/src/gsnap.c:222:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char CMET_FWD_CHARTABLE[4] = {'A','T','G','T'}; /* CT */
data/gmap-2020-11-20+ds/src/gsnap.c:223:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char CMET_REV_CHARTABLE[4] = {'A','C','A','T'}; /* GA */
data/gmap-2020-11-20+ds/src/gsnap.c:224:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char ATOI_FWD_CHARTABLE[4] = {'G','C','G','T'}; /* AG */
data/gmap-2020-11-20+ds/src/gsnap.c:225:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char ATOI_REV_CHARTABLE[4] = {'A','C','G','C'}; /* TC */
data/gmap-2020-11-20+ds/src/gsnap.c:1112:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acc[100+1], comma0[20], comma1[20], comma2[20], comma3[20], comma4[20], comma5[20];
data/gmap-2020-11-20+ds/src/gsnap.c:1303:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char threadname[12];
data/gmap-2020-11-20+ds/src/gsnap.c:1304:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acc[100+1], comma0[20], comma1[20], comma2[20], comma3[20], comma4[20], comma5[20];
data/gmap-2020-11-20+ds/src/gsnap.c:1305:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(threadname,"thread-%ld",worker_id);
data/gmap-2020-11-20+ds/src/gsnap.c:1764:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
required_index1interval = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1774:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
maxpaths_search = atoi(optarg);
data/gmap-2020-11-20+ds/src/gsnap.c:1835:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
max_anchors = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1873:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
inbuffer_nspaces = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1876:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
output_buffer_size = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1879:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
barcode_length = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1882:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
endtrim_length = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1885:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
acc_fieldi_start = atoi(check_valid_int(optarg)) - 1;
data/gmap-2020-11-20+ds/src/gsnap.c:1892:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
acc_fieldi_end = atoi(check_valid_int(optarg)) - 1;
data/gmap-2020-11-20+ds/src/gsnap.c:1969:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pairmax_dna = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1972:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pairmax_rna = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1975:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
expected_pairlength = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1978:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pairlength_deviation = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:1995:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
min_indel_end_matches = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2001:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
antistranded_penalty = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2035:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
trim_indel_score = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2039:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
fusion_sensitivity = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2042:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
localsplicing_penalty = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2047:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
distantsplicing_penalty = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2054:36: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
min_distantsplicing_end_matches = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2057:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
min_shortend = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2091:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sam_headers_batch = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2211:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
required_index1part = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2268:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'M': subopt_levels = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2277:58: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'i': indel_penalty_middle = indel_penalty_end = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2295:36: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'Y': max_end_insertions = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2296:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'Z': max_end_deletions = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2314:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
distantsplicing_penalty = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2387:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 't': nthreads = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/gsnap.c:2410:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
quality_shift = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/gsnap.c:2420:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
MAPQ_init(/*quality_score_adj*/atoi(check_valid_int(optarg)));
data/gmap-2020-11-20+ds/src/gsnap.c:2426:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'n': maxpaths_report = atoi(check_valid_int(optarg)); break;
data/gmap-2020-11-20+ds/src/iit-read-univ.c:585:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char EMPTY_STRING[1] = {'\0'};
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1328:18: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((new->fd = open(filename,O_RDONLY,0764)) < 0) {
data/gmap-2020-11-20+ds/src/iit-read.c:483:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char EMPTY_STRING[1] = {'\0'};
data/gmap-2020-11-20+ds/src/iit-read.c:2361:18: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((new->fd = open(filename,O_RDONLY,0764)) < 0) {
data/gmap-2020-11-20+ds/src/iit-write-univ.c:7:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write-univ.c:7:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write-univ.c:10:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write-univ.c:274:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(intervals[i]),List_head(p),sizeof(struct Univinterval_T));
data/gmap-2020-11-20+ds/src/iit-write-univ.c:315:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&((*intervals)[i]),List_head(p),sizeof(struct Univinterval_T));
data/gmap-2020-11-20+ds/src/iit-write.c:7:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write.c:7:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write.c:10:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/iit-write.c:287:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(intervals[i]),List_head(p),sizeof(struct Interval_T));
data/gmap-2020-11-20+ds/src/iit-write.c:326:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&((*intervals)[i]),List_head(p),sizeof(struct Interval_T));
data/gmap-2020-11-20+ds/src/iit_get.c:167:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/iit_get.c:405:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
value = atoi(label);
data/gmap-2020-11-20+ds/src/iit_get.c:1014:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'u': nflanking = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/iit_get.c:1016:46: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'c': centerp = true; centerlength = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/iit_store.c:820:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *line, Space[1000], *columns[GFF3_COLUMNS];
data/gmap-2020-11-20+ds/src/iit_store.c:889:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Space,"gff.%d",row);
data/gmap-2020-11-20+ds/src/iit_store.c:893:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Space,"gff.%d",row);
data/gmap-2020-11-20+ds/src/iit_store.c:976:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'v': iit_version = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/iit_store.c:1038:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(typestring,"circular");
data/gmap-2020-11-20+ds/src/iit_store.c:1058:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(typestring,"circular");
data/gmap-2020-11-20+ds/src/indexdb-cat.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb-cat.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb-cat.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb-cat.c:668:37: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': required_index1part = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/indexdb-cat.c:669:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': required_index1interval = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/indexdb-cat.c:702:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
filename = (char *) CALLOC(strlen(argv[genomei])+strlen("/")+
data/gmap-2020-11-20+ds/src/indexdb-write.c:7:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb-write.c:7:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb-write.c:10:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/indexdb.c:439:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *pattern, interval_char, digit_string[2], *p, *q;
data/gmap-2020-11-20+ds/src/indexdb.c:494:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:497:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:505:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part = 10*atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:507:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part += atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:510:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:523:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:724:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char interval_char, digit_string[2], *p, *q;
data/gmap-2020-11-20+ds/src/indexdb.c:831:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:834:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:844:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_basesize = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:847:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:850:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:917:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part = 10*atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:919:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_index1part += atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:922:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/indexdb.c:1836:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4];
data/gmap-2020-11-20+ds/src/indexdb.c:1857:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buffer[4];
data/gmap-2020-11-20+ds/src/indexdb.c:1916:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buffer[4];
data/gmap-2020-11-20+ds/src/indexdb.c:1960:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4];
data/gmap-2020-11-20+ds/src/indexdb.c:2278:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(positions,&(this->positions[ptr0]),(*nentries)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/indexdb.c:2317:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(positions,&(this->positions[ptr0]),(*nentries)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/indexdb.c:2442:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(positions,&(this->positions[ptr0]),(*nentries)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/indexdb.c:2482:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(positions,&(this->positions[ptr0]),(*nentries)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect-large.c:387:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect-large.c:417:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect-large.c:449:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect-large.c:475:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect.c:502:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/intersect.c:537:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/intersect.c:566:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/intersect.c:591:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/intersect.c:733:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect.c:762:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect.c:791:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intersect.c:816:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(more_diagonals,diagonals,guess_allocation*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/intlist.c:434:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *string, Buffer[256];
data/gmap-2020-11-20+ds/src/intlist.c:444:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%d,",Intlist_head(p));
data/gmap-2020-11-20+ds/src/intlist.c:447:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%d",Intlist_head(p));
data/gmap-2020-11-20+ds/src/intlist.c:453:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%d,",Intlist_head(p));
data/gmap-2020-11-20+ds/src/intlist.c:456:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%d",Intlist_head(p));
data/gmap-2020-11-20+ds/src/junction.c:373:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/kmer-search.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/kmer-search.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/knownsplicing.c:260:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer_ref[17], gbuffer_alt[17], *chr;
data/gmap-2020-11-20+ds/src/ladder.c:672:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(stream,source->byscore[score],(source->nhits[score]+1)*sizeof(Stage3end_T));
data/gmap-2020-11-20+ds/src/ladder.c:679:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(stream,oldstream,(length+1)*sizeof(Stage3end_T));
data/gmap-2020-11-20+ds/src/ladder.c:719:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(stream,oldstream,(length+1)*sizeof(Stage3end_T));
data/gmap-2020-11-20+ds/src/ladder.c:730:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(byscore[score],source->byscore[score],(nhits[score]+1)*sizeof(Stage3end_T));
data/gmap-2020-11-20+ds/src/ladder.c:736:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(stream,oldstream,(length+1)*sizeof(Stage3end_T));
data/gmap-2020-11-20+ds/src/littleendian.c:11:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[1];
data/gmap-2020-11-20+ds/src/littleendian.c:21:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/littleendian.c:35:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[8];
data/gmap-2020-11-20+ds/src/littleendian.c:54:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buf[4];
data/gmap-2020-11-20+ds/src/match.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/match.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/match.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/maxent_hr.c:24667:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/md5.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/md5.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/md5.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/md5.c:37:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char PADDING[64] = {
data/gmap-2020-11-20+ds/src/md5.c:104:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
transform (UINT4 state[4], unsigned char block[64]) {
data/gmap-2020-11-20+ds/src/md5.c:193:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char buffer[64];
data/gmap-2020-11-20+ds/src/md5.c:208:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) &(buffer[index]),input,part_len);
data/gmap-2020-11-20+ds/src/md5.c:221:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) &(buffer[index]),&(input[i]),input_len-i);
data/gmap-2020-11-20+ds/src/md5.c:229:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char bits[8];
data/gmap-2020-11-20+ds/src/mdprint.c:23:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/merge-diagonals-heap.c:261:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(copy,stream,nelts*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/merge-diagonals-heap.c:302:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result,stream,(*nelts)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:154:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(out,stream_array[order[k]],n*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:185:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(heap[heapi],stream_array[order[i]],n*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:252:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result,stream,(*nelts1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:354:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(out,stream_array[order[k]],n*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:384:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(heap[heapi],stream_array[order[i]],n*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint4.c:446:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result,stream,(*nelts1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint8.c:362:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(out,stream_array[order[k]],n*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint8.c:384:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(heap[heapi],stream_array[order[i]],n*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/merge-diagonals-simd-uint8.c:445:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result,stream,(*nelts1)*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/merge-uint4.c:534:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(C,A,(Aend - A) * sizeof(unsigned int));
data/gmap-2020-11-20+ds/src/merge-uint4.c:535:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(C,B,(Bend - B) * sizeof(unsigned int));
data/gmap-2020-11-20+ds/src/merge-uint8.c:412:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(C,A,(Aend - A) * sizeof(UINT8));
data/gmap-2020-11-20+ds/src/merge-uint8.c:413:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(C,B,(Bend - B) * sizeof(UINT8));
data/gmap-2020-11-20+ds/src/oligo.c:407:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+0],((Oligospace_T[]){/* */RIGHT_A, /* */RIGHT_C, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:408:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+0],((Oligospace_T[]){/* */LEFT_A, /* */LEFT_C, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:410:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+0],((Oligospace_T[]){/* */LEFT_T, /* */LEFT_G, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:411:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+0],((Oligospace_T[]){/* */RIGHT_T, /* */RIGHT_G, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:414:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+0],((Oligospace_T[]){/* */RIGHT_A, /*C>T*/RIGHT_T, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:415:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+0],((Oligospace_T[]){/* */LEFT_A, /*C>T*/LEFT_T, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:417:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+0],((Oligospace_T[]){/* */LEFT_T, /*G>A*/LEFT_A, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:418:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+0],((Oligospace_T[]){/* */RIGHT_T, /*G>A*/RIGHT_A, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:430:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+1],((Oligospace_T[]){/* */RIGHT_A, /*C>T*/RIGHT_T, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:431:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+2],((Oligospace_T[]){/* */RIGHT_A, /* */RIGHT_C, /*G>A*/RIGHT_A, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:433:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+1],((Oligospace_T[]){/* */LEFT_A, /*C>T*/LEFT_T, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:434:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+2],((Oligospace_T[]){/* */LEFT_A, /* */LEFT_C, /*G>A*/LEFT_A, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:437:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+1],((Oligospace_T[]){/* */LEFT_T, /*G>A*/LEFT_A, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:438:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+2],((Oligospace_T[]){/* */LEFT_T, /* */LEFT_G, /*C>T*/LEFT_T, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:440:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+1],((Oligospace_T[]){/* */RIGHT_T, /*G>A*/RIGHT_A, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:441:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+2],((Oligospace_T[]){/* */RIGHT_T, /* */RIGHT_G, /*C>T*/RIGHT_T, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:444:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+0],((Oligospace_T[]){/*A>G*/RIGHT_G, /* */RIGHT_C, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:445:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+0],((Oligospace_T[]){/*A>G*/LEFT_G, /* */LEFT_C, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:447:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+0],((Oligospace_T[]){/*T>C*/LEFT_C, /* */LEFT_G, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:448:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+0],((Oligospace_T[]){/*T>C*/RIGHT_C, /* */RIGHT_G, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:451:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+1],((Oligospace_T[]){/*A>G*/RIGHT_G, /* */RIGHT_C, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:452:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+2],((Oligospace_T[]){/* */RIGHT_A, /* */RIGHT_C, /* */RIGHT_G, /*T>C*/RIGHT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:454:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+1],((Oligospace_T[]){/*A>G*/LEFT_G, /* */LEFT_C, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:455:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+2],((Oligospace_T[]){/* */LEFT_A, /* */LEFT_C, /* */LEFT_G, /*T>C*/LEFT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:458:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+1],((Oligospace_T[]){/*T>C*/LEFT_C, /* */LEFT_G, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:459:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+2],((Oligospace_T[]){/* */LEFT_T, /* */LEFT_G, /* */LEFT_C, /*A>G*/LEFT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:461:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+1],((Oligospace_T[]){/*T>C*/RIGHT_C, /* */RIGHT_G, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:462:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+2],((Oligospace_T[]){/* */RIGHT_T, /* */RIGHT_G, /* */RIGHT_C, /*A>G*/RIGHT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:465:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+0],((Oligospace_T[]){/* */RIGHT_A, /* */RIGHT_C, /* */RIGHT_G, /*T>C*/RIGHT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:466:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+0],((Oligospace_T[]){/* */LEFT_A, /* */LEFT_C, /* */LEFT_G, /*T>C*/LEFT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:468:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+0],((Oligospace_T[]){/* */LEFT_T, /* */LEFT_G, /* */LEFT_C, /*A>G*/LEFT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:469:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+0],((Oligospace_T[]){/* */RIGHT_T, /* */RIGHT_G, /* */RIGHT_C, /*A>G*/RIGHT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:472:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+1],((Oligospace_T[]){/* */RIGHT_A, /* */RIGHT_C, /* */RIGHT_G, /*T>C*/RIGHT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:473:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_5[+2],((Oligospace_T[]){/*A>G*/RIGHT_G, /* */RIGHT_C, /* */RIGHT_G, /* */RIGHT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:475:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+1],((Oligospace_T[]){/* */LEFT_A, /* */LEFT_C, /* */LEFT_G, /*T>C*/LEFT_C}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:476:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv_3[+2],((Oligospace_T[]){/*A>G*/LEFT_G, /* */LEFT_C, /* */LEFT_G, /* */LEFT_T}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:479:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+1],((Oligospace_T[]){/* */LEFT_T, /* */LEFT_G, /* */LEFT_C, /*A>G*/LEFT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:480:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_5[+2],((Oligospace_T[]){/*T>C*/LEFT_C, /* */LEFT_G, /* */LEFT_C, /* */LEFT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:482:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+1],((Oligospace_T[]){/* */RIGHT_T, /* */RIGHT_G, /* */RIGHT_C, /*A>G*/RIGHT_G}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligo.c:483:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv_3[+2],((Oligospace_T[]){/*T>C*/RIGHT_C, /* */RIGHT_G, /* */RIGHT_C, /* */RIGHT_A}),4*sizeof(Oligospace_T));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:8854:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[33];
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:32623:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(Chrpos_T *));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:32861:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(Chrpos_T *));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:33049:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(Chrpos_T *));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:33750:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) pointers,positions,oligospace*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:33865:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) working_counts,(const void *) this->counts,this->oligospace*sizeof(Count_T));
data/gmap-2020-11-20+ds/src/oligoindex_hr.c:33900:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) working_counts,(const void *) this->counts,this->oligospace*sizeof(Count_T));
data/gmap-2020-11-20+ds/src/orderstat.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/orderstat.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/orderstat.c:162:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) temp,vector,n*sizeof(double));
data/gmap-2020-11-20+ds/src/orderstat.c:176:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) temp,vector,n*sizeof(int));
data/gmap-2020-11-20+ds/src/orderstat.c:190:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) temp,vector,n*sizeof(long int));
data/gmap-2020-11-20+ds/src/orderstat.c:276:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
n = atoi(argv[1]);
data/gmap-2020-11-20+ds/src/outbuffer.c:173:31: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output_failedinput_1 = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/outbuffer.c:180:31: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output_failedinput_2 = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/outbuffer.c:187:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output_failedinput = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/outbuffer.c:197:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output_failedinput = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/pair.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/pair.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/pair.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/pair.c:467:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) &(source[k++]),(void *) &(source[i]),sizeof(struct T));
data/gmap-2020-11-20+ds/src/pair.c:753:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[100];
data/gmap-2020-11-20+ds/src/pair.c:757:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",(unsigned long long) (chroffset+this->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:782:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[100];
data/gmap-2020-11-20+ds/src/pair.c:786:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",(unsigned long long) (chroffset+this->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:812:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[100];
data/gmap-2020-11-20+ds/src/pair.c:815:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",(unsigned long long) (chroffset + start->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:822:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",(unsigned long long) (chroffset + end->genomepos + ONEBASEDP));
data/gmap-2020-11-20+ds/src/pair.c:853:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/pair.c:862:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(new[j]),&(old[i]),sizeof(struct T));
data/gmap-2020-11-20+ds/src/pair.c:875:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(new[j]),&(old[i]),sizeof(struct T));
data/gmap-2020-11-20+ds/src/pair.c:893:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&(new[j]),&(old[i]),sizeof(struct T));
data/gmap-2020-11-20+ds/src/pair.c:909:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char intronstring[20], cdnabreak[20], genomicbreak[20], comp;
data/gmap-2020-11-20+ds/src/pair.c:933:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cdnabreak,"%d",(this->querypos - last_querypos) - 1);
data/gmap-2020-11-20+ds/src/pair.c:935:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cdnabreak,"%d",(last_querypos - this->querypos) - 1);
data/gmap-2020-11-20+ds/src/pair.c:938:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(genomicbreak,"%d",last_genomepos - this->genomepos - 1);
data/gmap-2020-11-20+ds/src/pair.c:940:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(genomicbreak,"%d",this->genomepos - last_genomepos - 1);
data/gmap-2020-11-20+ds/src/pair.c:968:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intronstring,"%d",last_genomepos - this->genomepos - 1);
data/gmap-2020-11-20+ds/src/pair.c:970:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intronstring,"%d",this->genomepos - last_genomepos - 1);
data/gmap-2020-11-20+ds/src/pair.c:2923:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1];
data/gmap-2020-11-20+ds/src/pair.c:3040:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"M%d",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:3043:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"I%d",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:3046:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"D%d",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:3091:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"N%u",(intron_end - intron_start) + 1);
data/gmap-2020-11-20+ds/src/pair.c:3093:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"N%u",(intron_start - intron_end) + 1);
data/gmap-2020-11-20+ds/src/pair.c:3115:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"M%d",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:3120:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"D%d",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:3127:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"M%d",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:3131:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"I%d",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:3150:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"I%d",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:3154:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"D%d",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:3211:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"M%d",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:3214:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"I%d",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:3217:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"D%d",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5014:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1], *curr_token, *last_token;
data/gmap-2020-11-20+ds/src/pair.c:5023:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/pair.c:5032:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/pair.c:5034:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d%c",length,last_type);
data/gmap-2020-11-20+ds/src/pair.c:5048:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/pair.c:5050:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d%c",length,last_type);
data/gmap-2020-11-20+ds/src/pair.c:5141:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1];
data/gmap-2020-11-20+ds/src/pair.c:5163:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5169:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5175:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5179:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",ptr->querypos - (*hardclip_start));
data/gmap-2020-11-20+ds/src/pair.c:5208:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:5211:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5214:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5253:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5256:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5259:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5266:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5269:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5272:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5276:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5279:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5283:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5296:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"0M");
data/gmap-2020-11-20+ds/src/pair.c:5300:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uI",query_gap);
data/gmap-2020-11-20+ds/src/pair.c:5313:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:5318:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5326:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:5330:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5344:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5348:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5372:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/pair.c:5375:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5378:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5389:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5395:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5401:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos);
data/gmap-2020-11-20+ds/src/pair.c:5405:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5422:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1];
data/gmap-2020-11-20+ds/src/pair.c:5444:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5450:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5456:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/pair.c:5460:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",ptr->querypos - (*hardclip_start));
data/gmap-2020-11-20+ds/src/pair.c:5489:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/pair.c:5492:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/pair.c:5495:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5498:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5537:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5540:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5543:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5550:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5553:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5556:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5560:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5563:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5567:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/pair.c:5580:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"0M");
data/gmap-2020-11-20+ds/src/pair.c:5584:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uI",query_gap);
data/gmap-2020-11-20+ds/src/pair.c:5597:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/pair.c:5601:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/pair.c:5606:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5614:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/pair.c:5618:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/pair.c:5622:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5636:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5640:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5657:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/pair.c:5669:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/pair.c:5694:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/pair.c:5697:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/pair.c:5700:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/pair.c:5703:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/pair.c:5714:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5720:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5726:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos);
data/gmap-2020-11-20+ds/src/pair.c:5730:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/pair.c:5946:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *cigar_token, token[MAX_INT_DIGITS+CHAR_DIGITS+1], *first_token, type;
data/gmap-2020-11-20+ds/src/pair.c:5962:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length = atoi(cigar_token);
data/gmap-2020-11-20+ds/src/pair.c:5980:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:5991:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",tolower(this->genome));
data/gmap-2020-11-20+ds/src/pair.c:5995:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",this->genome);
data/gmap-2020-11-20+ds/src/pair.c:6020:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6031:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",this->genome);
data/gmap-2020-11-20+ds/src/pair.c:6045:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6057:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length = atoi(cigar_token);
data/gmap-2020-11-20+ds/src/pair.c:6079:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6089:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",tolower(complCode[(int) this->genome]));
data/gmap-2020-11-20+ds/src/pair.c:6092:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6129:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6139:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6152:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6684:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1], *first_token;
data/gmap-2020-11-20+ds/src/pair.c:6708:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6718:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",watsonp ? this->genome : complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6733:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6745:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",watsonp ? this->genome : complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6757:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6781:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6791:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",watsonp ? this->genome : complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6809:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pair.c:6820:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",watsonp ? this->genome : complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/pair.c:6832:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/pairpool.c:279:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pair,orig,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/pairpool.c:683:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest,source,npairs*sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/pairpool.c:1014:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/pairpool.c:1208:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pair,orig,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/path-solve.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/path-solve.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb-write.c:7:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb-write.c:7:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb-write.c:10:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb-write.c:470:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->offsets,source->offsets,offsets_size*sizeof(UINT2));
data/gmap-2020-11-20+ds/src/regiondb-write.c:471:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->positions,source->positions,REGION_LENGTH*sizeof(UINT2));
data/gmap-2020-11-20+ds/src/regiondb-write.c:589:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen((file = *files++),"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/regiondb-write.c:615:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((fp = fopen((file = *files++),"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/regiondb.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/regiondb.c:1502:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char interval_char, digit_string[2], *p, *q;
data/gmap-2020-11-20+ds/src/regiondb.c:1555:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_region1part = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1558:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1568:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_basesize = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1571:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_region1part = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1574:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1633:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_region1part = 10*atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1635:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_region1part += atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1638:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
found_interval = atoi(digit_string);
data/gmap-2020-11-20+ds/src/regiondb.c:1866:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+0],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1867:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+0],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1870:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+0],((Localspace_T[]){/* */VALUE_A, /*C>T*/VALUE_T, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1871:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+0],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /*G>A*/VALUE_A, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1882:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+1],((Localspace_T[]){/* */VALUE_A, /*C>T*/VALUE_T, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1883:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+2],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /*G>A*/VALUE_A, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1885:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+1],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /*G>A*/VALUE_A, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1886:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+2],((Localspace_T[]){/* */VALUE_A, /*C>T*/VALUE_T, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1889:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+0],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1890:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+0],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1893:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+1],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1894:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+2],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1896:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+1],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1897:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+2],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1900:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+0],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1901:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+0],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1904:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+1],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1905:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(forward_conv[+2],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1907:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+1],((Localspace_T[]){/*A>G*/VALUE_G, /* */VALUE_C, /* */VALUE_G, /* */VALUE_T}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/regiondb.c:1908:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(revcomp_conv[+2],((Localspace_T[]){/* */VALUE_A, /* */VALUE_C, /* */VALUE_G, /*T>C*/VALUE_C}),4*sizeof(Localspace_T));
data/gmap-2020-11-20+ds/src/sam_sort.c:353:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/sam_sort.c:500:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[CHUNK];
data/gmap-2020-11-20+ds/src/sam_sort.c:896:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[OUTPUTLEN], *ptr;
data/gmap-2020-11-20+ds/src/sam_sort.c:1637:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(orig_cells,cells,ncells_total*sizeof(T));
data/gmap-2020-11-20+ds/src/sam_sort.c:1861:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BUFFERLEN], *lastp, *p;
data/gmap-2020-11-20+ds/src/sam_sort.c:1944:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
output_nlines = atoi(check_valid_int(optarg));
data/gmap-2020-11-20+ds/src/sam_sort.c:2008:30: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((sam_inputs[filei] = fopen(argv[filei],"r")) == NULL) {
data/gmap-2020-11-20+ds/src/samheader.c:32:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/samheader.c:94:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((output = fopen(filename,write_mode)) == NULL) {
data/gmap-2020-11-20+ds/src/samheader.c:110:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[CHUNK], c, c0, c1, c2;
data/gmap-2020-11-20+ds/src/samprint.c:75:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/samread.c:37:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/samread.c:1181:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char flag_string[FLAGLEN], newflag_string[FLAGLEN];
data/gmap-2020-11-20+ds/src/samread.c:1184:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(flag_string,"%u",flag);
data/gmap-2020-11-20+ds/src/samread.c:1186:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(newflag_string,"%u",flag | DUPLICATE_READ);
data/gmap-2020-11-20+ds/src/segment-search.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/segment-search.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/segment-search.c:9:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/segment-search.c:810:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(diagonals_used,diagonals_alloc,used_npositions*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/segment-search.c:943:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(diagonals_used,diagonals_alloc,used_npositions*sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/sequence.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/sequence.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/sequence.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/sequence.c:324:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char *iupac_table[21+1] =
data/gmap-2020-11-20+ds/src/sequence.c:349:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char aa_table[21+1] = "ACDEFGHIKLMNPQRSTVWY*U";
data/gmap-2020-11-20+ds/src/sequence.c:455:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Header[HEADERLEN];
data/gmap-2020-11-20+ds/src/sequence.c:456:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Discard[DISCARDLEN];
data/gmap-2020-11-20+ds/src/sequence.c:458:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Sequence[1+MAXSEQLEN+1]; /* Used by Sequence_read_unlimited */
data/gmap-2020-11-20+ds/src/sequence.c:459:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Sequence1[HALFLEN+1]; /* 1 at end for '\0' */
data/gmap-2020-11-20+ds/src/sequence.c:460:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Sequence2[HALFLEN+3]; /* 1 at end for '\0' and 2 extra in cyclic part for '\n' and '\0' */
data/gmap-2020-11-20+ds/src/sequence.c:565:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(this->acc,"NO_HEADER");
data/gmap-2020-11-20+ds/src/sequence.c:1014:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/sequence.c:1051:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/sequence.c:1202:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/sequence.c:1204:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/sequence.c:1745:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/sequence.c:1781:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/sequence.c:1817:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/sequence.c:1863:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/sequence.c:2009:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(gbuffer,&(usersegment->contents[left]),length*sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/shortread.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/shortread.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/shortread.c:213:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Header[HEADERLEN];
data/gmap-2020-11-20+ds/src/shortread.c:214:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Discard[DISCARDLEN];
data/gmap-2020-11-20+ds/src/shortread.c:220:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Read1[MAX_EXPECTED_READLENGTH+1];
data/gmap-2020-11-20+ds/src/shortread.c:221:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Read2[MAX_EXPECTED_READLENGTH+1];
data/gmap-2020-11-20+ds/src/shortread.c:222:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char Quality[MAX_EXPECTED_READLENGTH+1];
data/gmap-2020-11-20+ds/src/shortread.c:1328:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/shortread.c:1348:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/shortread.c:1382:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_STD;
data/gmap-2020-11-20+ds/src/shortread.c:1384:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/shortread.c:1607:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4];
data/gmap-2020-11-20+ds/src/shortread.c:1627:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer,"D%d",jump[i][j]);
data/gmap-2020-11-20+ds/src/shortread.c:1629:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer,"H%d",jump[i][j]);
data/gmap-2020-11-20+ds/src/shortread.c:1631:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer,"V%d",jump[i][j]);
data/gmap-2020-11-20+ds/src/shortread.c:1633:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer,"S%d",0);
data/gmap-2020-11-20+ds/src/simplepair.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/simplepair.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/simplepair.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/simplepair.c:438:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1], *curr_token, *last_token;
data/gmap-2020-11-20+ds/src/simplepair.c:447:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/simplepair.c:456:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/simplepair.c:458:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d%c",length,last_type);
data/gmap-2020-11-20+ds/src/simplepair.c:472:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length += atoi(last_token);
data/gmap-2020-11-20+ds/src/simplepair.c:474:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d%c",length,last_type);
data/gmap-2020-11-20+ds/src/simplepair.c:527:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1];
data/gmap-2020-11-20+ds/src/simplepair.c:549:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:555:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:561:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:565:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",ptr->querypos - (*hardclip_start));
data/gmap-2020-11-20+ds/src/simplepair.c:594:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/simplepair.c:597:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:600:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:639:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:642:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:645:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:652:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:655:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:658:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:662:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:665:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:669:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:682:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"0M");
data/gmap-2020-11-20+ds/src/simplepair.c:686:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uI",query_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:699:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/simplepair.c:704:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:712:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/simplepair.c:716:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:730:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:734:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:758:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dM",Mlength);
data/gmap-2020-11-20+ds/src/simplepair.c:761:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:764:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:775:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:781:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:787:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos);
data/gmap-2020-11-20+ds/src/simplepair.c:791:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:808:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char token[MAX_INT_DIGITS+CHAR_DIGITS+1];
data/gmap-2020-11-20+ds/src/simplepair.c:830:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:836:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:842:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_start);
data/gmap-2020-11-20+ds/src/simplepair.c:846:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",ptr->querypos - (*hardclip_start));
data/gmap-2020-11-20+ds/src/simplepair.c:875:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/simplepair.c:878:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/simplepair.c:881:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:884:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:923:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:926:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:929:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:936:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:939:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:942:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:946:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:949:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uD",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:953:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uN",genome_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:966:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"0M");
data/gmap-2020-11-20+ds/src/simplepair.c:970:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%uI",query_gap);
data/gmap-2020-11-20+ds/src/simplepair.c:983:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/simplepair.c:987:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/simplepair.c:992:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1000:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/simplepair.c:1004:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1008:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:1022:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:1026:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1043:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/simplepair.c:1055:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1080:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d=",Elength);
data/gmap-2020-11-20+ds/src/simplepair.c:1083:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dX",Xlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1086:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dI",Ilength);
data/gmap-2020-11-20+ds/src/simplepair.c:1089:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dD",Dlength);
data/gmap-2020-11-20+ds/src/simplepair.c:1100:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:1106:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:1112:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos);
data/gmap-2020-11-20+ds/src/simplepair.c:1116:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%dH",*hardclip_end);
data/gmap-2020-11-20+ds/src/simplepair.c:1140:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/simplepair.c:1146:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *cigar_token, token[MAX_INT_DIGITS+CHAR_DIGITS+1], *first_token, type;
data/gmap-2020-11-20+ds/src/simplepair.c:1162:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length = atoi(cigar_token);
data/gmap-2020-11-20+ds/src/simplepair.c:1180:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/simplepair.c:1191:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",tolower(this->genome));
data/gmap-2020-11-20+ds/src/simplepair.c:1195:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",this->genome);
data/gmap-2020-11-20+ds/src/simplepair.c:1220:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/simplepair.c:1231:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",this->genome);
data/gmap-2020-11-20+ds/src/simplepair.c:1245:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/simplepair.c:1257:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
length = atoi(cigar_token);
data/gmap-2020-11-20+ds/src/simplepair.c:1279:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/simplepair.c:1289:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",tolower(complCode[(int) this->genome]));
data/gmap-2020-11-20+ds/src/simplepair.c:1292:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/simplepair.c:1329:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/simplepair.c:1339:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%c",complCode[(int) this->genome]);
data/gmap-2020-11-20+ds/src/simplepair.c:1352:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(token,"%d",nmatches);
data/gmap-2020-11-20+ds/src/snpindex.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/snpindex.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/snpindex.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/snpindex.c:1259:37: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'k': required_index1part = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/snpindex.c:1260:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': required_interval = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/snpindex.c:1263:30: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'w': max_warnings = atoi(optarg); break;
data/gmap-2020-11-20+ds/src/snpindex.c:1350:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(snp_blocks,Genome_blocks(genome),nuint4*sizeof(Genomecomp_T));
data/gmap-2020-11-20+ds/src/splicetrie_build.c:120:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer[17];
data/gmap-2020-11-20+ds/src/splicetrie_build.c:399:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer_ref[17], gbuffer_alt[17], *chr;
data/gmap-2020-11-20+ds/src/splicetrie_build.c:817:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer_ref[17], gbuffer_alt[17], *chr;
data/gmap-2020-11-20+ds/src/splicetrie_build.c:2843:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer[17];
data/gmap-2020-11-20+ds/src/stage1hr.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/stage1hr.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/stage1hr.c:9:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/stage1hr.c:967:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/stage1hr.h:88:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char *plus_rawpositions_high_5[6];
data/gmap-2020-11-20+ds/src/stage1hr.h:89:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char *minus_rawpositions_high_5[6];
data/gmap-2020-11-20+ds/src/stage1hr.h:90:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char *plus_rawpositions_high_3[6];
data/gmap-2020-11-20+ds/src/stage1hr.h:91:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char *minus_rawpositions_high_3[6];
data/gmap-2020-11-20+ds/src/stage2.c:4116:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/stage3.c:1384:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/stage3.c:5067:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newpair++,oldpair,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/stage3.c:5144:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newpair++,oldpair,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/stage3.c:5223:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newpair++,oldpair,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/stage3.c:5239:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newpair++,oldpair,sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/stage3.c:5918:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->pairarray,old->pairarray,old->npairs*sizeof(struct Pair_T));
data/gmap-2020-11-20+ds/src/stage3.c:6835:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/stage3.c:12062:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gbuffer1[MAXENT_MAXLENGTH];
data/gmap-2020-11-20+ds/src/stage3hr.c:3208:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/stage3hr.c:10773:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newpair++,oldpair,sizeof(struct Simplepair_T));
data/gmap-2020-11-20+ds/src/substring.c:195:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_LC;
data/gmap-2020-11-20+ds/src/substring.c:3813:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->alts_coords,old->alts_coords,old->alts_ncoords * sizeof(Univcoord_T));
data/gmap-2020-11-20+ds/src/substring.c:3814:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->alts_knowni,old->alts_knowni,old->alts_ncoords * sizeof(int));
data/gmap-2020-11-20+ds/src/substring.c:3815:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->alts_nmismatches,old->alts_nmismatches,old->alts_ncoords * sizeof(int));
data/gmap-2020-11-20+ds/src/substring.c:3816:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->alts_ref_nmismatches,old->alts_ref_nmismatches,old->alts_ncoords * sizeof(int));
data/gmap-2020-11-20+ds/src/substring.c:3817:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->alts_probs,old->alts_probs,old->alts_ncoords * sizeof(double));
data/gmap-2020-11-20+ds/src/terminal.c:6:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/terminal.c:6:23: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/terminal.c:9:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/transcriptome.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/transcriptome.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/transcriptome.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/transcriptome.c:123:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename,"rb")) == NULL) {
data/gmap-2020-11-20+ds/src/translation.c:70:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char complCode[128] = COMPLEMENT_UC;
data/gmap-2020-11-20+ds/src/translation.c:71:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char uppercaseCode[128] = UPPERCASE_U2T;
data/gmap-2020-11-20+ds/src/translation.c:2442:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char nt_genomicseg[MAXMUT], aa_genomicseg[MAXMUT], nt_queryseq[MAXMUT], aa_queryseq[MAXMUT];
data/gmap-2020-11-20+ds/src/trindex.c:6:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/trindex.c:6:24: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memcpy(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/trindex.c:9:25: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define memmove(d,s,n) bcopy((s),(d),(n))
data/gmap-2020-11-20+ds/src/trindex.c:110:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[BUF_SIZE];
data/gmap-2020-11-20+ds/src/trindex.c:195:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in = open(alignment_file, O_RDONLY);
data/gmap-2020-11-20+ds/src/trindex.c:199:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out = open(filename,/*openFlags*/O_CREAT | O_WRONLY | O_TRUNC,
data/gmap-2020-11-20+ds/src/trindex.c:246:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(filename,"wb");
data/gmap-2020-11-20+ds/src/trindex.c:285:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(filename,"wb");
data/gmap-2020-11-20+ds/src/uint8list.c:272:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *string, Buffer[256];
data/gmap-2020-11-20+ds/src/uint8list.c:282:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu,",Uint8list_head(p));
data/gmap-2020-11-20+ds/src/uint8list.c:285:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",Uint8list_head(p));
data/gmap-2020-11-20+ds/src/uint8list.c:291:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu,",Uint8list_head(p));
data/gmap-2020-11-20+ds/src/uint8list.c:294:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",Uint8list_head(p));
data/gmap-2020-11-20+ds/src/uint8list.c:304:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *string, Buffer[256];
data/gmap-2020-11-20+ds/src/uint8list.c:314:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu,",Uint8list_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uint8list.c:317:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",Uint8list_head(p));
data/gmap-2020-11-20+ds/src/uint8list.c:323:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu,",Uint8list_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uint8list.c:326:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%llu",Uint8list_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uint8table_rh.c:195:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->saved_contents,old_saved_contents,this->size * sizeof(void *));
data/gmap-2020-11-20+ds/src/uintlist.c:273:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *string, Buffer[256];
data/gmap-2020-11-20+ds/src/uintlist.c:283:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u,",Uintlist_head(p));
data/gmap-2020-11-20+ds/src/uintlist.c:286:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u",Uintlist_head(p));
data/gmap-2020-11-20+ds/src/uintlist.c:292:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u,",Uintlist_head(p));
data/gmap-2020-11-20+ds/src/uintlist.c:295:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u",Uintlist_head(p));
data/gmap-2020-11-20+ds/src/uintlist.c:305:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *string, Buffer[256];
data/gmap-2020-11-20+ds/src/uintlist.c:315:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u,",Uintlist_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uintlist.c:318:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u",Uintlist_head(p));
data/gmap-2020-11-20+ds/src/uintlist.c:324:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u,",Uintlist_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uintlist.c:327:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Buffer,"%u",Uintlist_head(p) - chroffset);
data/gmap-2020-11-20+ds/src/uinttable_rh.c:203:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->saved_contents,old_saved_contents,this->size * sizeof(void *));
data/gmap-2020-11-20+ds/src/access.c:140:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(source)) != EOF) {
data/gmap-2020-11-20+ds/src/access.c:166:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c1 = fgetc(fp1);
data/gmap-2020-11-20+ds/src/access.c:167:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c2 = fgetc(fp2);
data/gmap-2020-11-20+ds/src/access.c:174:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c1 = fgetc(fp1);
data/gmap-2020-11-20+ds/src/access.c:175:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c2 = fgetc(fp2);
data/gmap-2020-11-20+ds/src/atoiindex.c:33:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/atoiindex.c:739:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:739:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:741:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:741:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:910:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:910:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:912:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:912:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1036:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1036:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1036:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1039:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1039:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1039:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1046:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/atoiindex.c:1046:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/atoiindex.c:1047:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1047:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1078:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1078:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1078:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1079:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1079:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1079:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1082:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1082:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1082:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1083:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1083:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1083:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1086:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1086:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1086:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1087:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1087:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1087:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1091:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1091:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1091:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1092:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1092:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1092:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2iag")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1108:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1108:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1108:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1109:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1125:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1125:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1125:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1126:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1126:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1126:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1129:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1129:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1129:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1130:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1130:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1130:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1133:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1133:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1133:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1134:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1134:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1134:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1138:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1138:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1138:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1139:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1139:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1139:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("a2itc")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/atoiindex.c:1154:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1154:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1154:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/atoiindex.c:1155:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/bigendian.c:299:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(fd,buf,4);
data/gmap-2020-11-20+ds/src/bigendian.c:484:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(fd,buf,8);
data/gmap-2020-11-20+ds/src/boyer-moore.c:538:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
querylen = strlen(query);
data/gmap-2020-11-20+ds/src/boyer-moore.c:539:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
textlen = strlen(text);
data/gmap-2020-11-20+ds/src/chrnum.c:29:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string = (char *) CALLOC(strlen(label)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/chrnum.c:41:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string = (char *) CALLOC(strlen(label)+2,sizeof(char));
data/gmap-2020-11-20+ds/src/chrom.c:108:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->string = (char *) MALLOC((strlen(string)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/chrom.c:144:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->alpha = (char *) CALLOC(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/chrom.c:149:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
} else if (strlen(new->alpha) == 0) {
data/gmap-2020-11-20+ds/src/chrom.c:176:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->alpha,string,(p - string)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:33:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/cmetindex.c:879:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:879:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:881:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:881:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1050:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1050:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1052:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1052:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1176:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1176:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1176:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(sourcedir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1179:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1179:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1179:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
destdir = (char *) MALLOC((strlen(user_destdir)+strlen("/")+strlen(dbroot)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1186:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/cmetindex.c:1186:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/cmetindex.c:1187:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1187:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1218:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1218:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1218:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1219:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1219:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1219:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1222:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1222:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1222:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1223:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1223:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1223:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1226:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1226:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1226:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1227:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1227:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1227:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1231:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1231:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1231:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1232:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1232:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1232:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metct")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1248:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1248:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1248:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1249:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1265:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1265:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1265:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1266:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1266:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1266:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->pointers_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1269:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1269:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1269:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1270:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1270:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1270:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->offsets_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1273:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1273:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1273:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1274:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1274:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1274:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1278:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1278:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1278:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1279:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1279:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1279:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen("metga")+strlen(ifilenames->positions_high_index1info_ptr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/cmetindex.c:1294:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1294:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1294:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/cmetindex.c:1295:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/compress-write.c:106:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(sequence_fp)) != EOF && isspace(c)) {
data/gmap-2020-11-20+ds/src/datadir.c:17:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/datadir.c:56:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
directory = (char *) MALLOC((strlen(dirbuffer)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:81:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
configfile = (char *) CALLOC(strlen(p->pw_dir)+strlen("/")+strlen(".gmaprc")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:81:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
configfile = (char *) CALLOC(strlen(p->pw_dir)+strlen("/")+strlen(".gmaprc")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:81:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
configfile = (char *) CALLOC(strlen(p->pw_dir)+strlen("/")+strlen(".gmaprc")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:123:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fileroot,filename,p-&(filename[0]));
data/gmap-2020-11-20+ds/src/datadir.c:189:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomedir = (char *) CALLOC(strlen(user_genomedir)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:194:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomedir = (char *) CALLOC(strlen(getenv("GMAPDB"))+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:206:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomedir = (char *) CALLOC(strlen(GMAPDB)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:231:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newgenomedir = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(dbrootdir)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:231:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newgenomedir = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(dbrootdir)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:231:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newgenomedir = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(dbrootdir)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:238:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) +
data/gmap-2020-11-20+ds/src/datadir.c:238:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) +
data/gmap-2020-11-20+ds/src/datadir.c:238:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) +
data/gmap-2020-11-20+ds/src/datadir.c:239:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".version") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:246:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*fileroot = (char *) CALLOC(strlen(dbroot)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:251:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomesubdir = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:251:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomesubdir = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:251:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
genomesubdir = (char *) CALLOC(strlen(genomedir) + strlen("/") + strlen(dbroot) + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:267:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir) + strlen("/") + strlen(*fileroot) + strlen(".version") + 1,
data/gmap-2020-11-20+ds/src/datadir.c:267:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir) + strlen("/") + strlen(*fileroot) + strlen(".version") + 1,
data/gmap-2020-11-20+ds/src/datadir.c:267:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir) + strlen("/") + strlen(*fileroot) + strlen(".version") + 1,
data/gmap-2020-11-20+ds/src/datadir.c:267:87: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir) + strlen("/") + strlen(*fileroot) + strlen(".version") + 1,
data/gmap-2020-11-20+ds/src/datadir.c:272:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*dbversion = (char *) CALLOC(strlen(dbroot)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:287:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
mapdir = (char *) CALLOC(strlen(user_mapdir)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:290:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
mapdir = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/datadir.c:290:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
mapdir = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/datadir.c:290:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
mapdir = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/datadir.c:291:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".maps")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:315:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pos += strlen(" ");
data/gmap-2020-11-20+ds/src/datadir.c:325:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pos += strlen(filename);
data/gmap-2020-11-20+ds/src/datadir.c:385:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(entry->d_name)+strlen("/")+
data/gmap-2020-11-20+ds/src/datadir.c:385:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(entry->d_name)+strlen("/")+
data/gmap-2020-11-20+ds/src/datadir.c:385:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(entry->d_name)+strlen("/")+
data/gmap-2020-11-20+ds/src/datadir.c:385:84: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomedir)+strlen("/")+strlen(entry->d_name)+strlen("/")+
data/gmap-2020-11-20+ds/src/datadir.c:386:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(entry->d_name)+strlen(".version")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:386:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(entry->d_name)+strlen(".version")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:390:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(entry->d_name)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/datadir.c:437:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(mapdir)+strlen("/")+strlen(entry->d_name)+1,
data/gmap-2020-11-20+ds/src/datadir.c:437:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(mapdir)+strlen("/")+strlen(entry->d_name)+1,
data/gmap-2020-11-20+ds/src/datadir.c:437:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(mapdir)+strlen("/")+strlen(entry->d_name)+1,
data/gmap-2020-11-20+ds/src/datadir.c:443:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(entry->d_name)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/dynprog_end.c:2852:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(splicejunction_test[splicelength]),&(rev_gsequence[-contlength+1]),contlength);
data/gmap-2020-11-20+ds/src/dynprog_end.c:3114:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(splicejunction_test,gsequence,contlength);
data/gmap-2020-11-20+ds/src/filestring.c:235:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,q,this->nleft);
data/gmap-2020-11-20+ds/src/filestring.c:245:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,q,stringlen);
data/gmap-2020-11-20+ds/src/filestring.c:279:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,q,this->nleft);
data/gmap-2020-11-20+ds/src/filestring.c:289:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,string,stringlen);
data/gmap-2020-11-20+ds/src/filestring.c:329:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,q,this->nleft);
data/gmap-2020-11-20+ds/src/filestring.c:339:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(this->ptr,string,stringlen);
data/gmap-2020-11-20+ds/src/filestring.c:394:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
transfer_string(this,q,strlen(q));
data/gmap-2020-11-20+ds/src/filestring.c:399:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
transfer_string_reverse(this,q,strlen(q));
data/gmap-2020-11-20+ds/src/filestring.c:404:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
transfer_string_revcomp(this,q,strlen(q));
data/gmap-2020-11-20+ds/src/filestring.c:462:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((stringlen = (int) strlen(string)) < precision) {
data/gmap-2020-11-20+ds/src/filestring.c:473:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((stringlen = (int) strlen(string)) < precision) {
data/gmap-2020-11-20+ds/src/filestring.c:484:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((stringlen = (int) strlen(string)) < precision) {
data/gmap-2020-11-20+ds/src/filestring.c:607:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
transfer_string(dest,source->string,strlen(source->string));
data/gmap-2020-11-20+ds/src/fopen.c:18:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
command = (char *) MALLOC((strlen(read_files_command) + strlen(" ") + strlen(filename) + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/fopen.c:18:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
command = (char *) MALLOC((strlen(read_files_command) + strlen(" ") + strlen(filename) + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/fopen.c:18:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
command = (char *) MALLOC((strlen(read_files_command) + strlen(" ") + strlen(filename) + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:342:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
make_complement_buffered(Complement,Buffer,strlen(Buffer));
data/gmap-2020-11-20+ds/src/genome-write.c:352:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
altstrain_offset -= strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:358:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
altstrain_offset += strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:365:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(unsigned long long) currposition,(unsigned long long) (currposition-strlen(segment))));
data/gmap-2020-11-20+ds/src/genome-write.c:366:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currposition -= (Univcoord_T) strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:368:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fwrite(segment,sizeof(char),strlen(segment),refgenome_fp);
data/gmap-2020-11-20+ds/src/genome-write.c:370:112: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nbadchars = Compress_update_file(nbadchars,refgenome_fp,segment,currposition,currposition + (Univcoord_T) strlen(segment),
data/gmap-2020-11-20+ds/src/genome-write.c:375:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(unsigned long long) currposition,(unsigned long long) (currposition+strlen(segment))));
data/gmap-2020-11-20+ds/src/genome-write.c:377:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fwrite(segment,sizeof(char),strlen(segment),refgenome_fp);
data/gmap-2020-11-20+ds/src/genome-write.c:379:112: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nbadchars = Compress_update_file(nbadchars,refgenome_fp,segment,currposition,currposition + (Univcoord_T) strlen(segment),
data/gmap-2020-11-20+ds/src/genome-write.c:382:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currposition += (Univcoord_T) strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:566:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = fgetc(input)) != EOF && c != '\n') {
data/gmap-2020-11-20+ds/src/genome-write.c:733:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
make_complement_buffered(Complement,Buffer,strlen(Buffer));
data/gmap-2020-11-20+ds/src/genome-write.c:743:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
altstrain_offset -= strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:749:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
altstrain_offset += strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:756:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(unsigned long long) currposition,(unsigned long long) currposition-strlen(segment)));
data/gmap-2020-11-20+ds/src/genome-write.c:757:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currposition -= strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:758:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nbadchars = Compress_update_memory(nbadchars,genomecomp,segment,currposition,currposition+strlen(segment));
data/gmap-2020-11-20+ds/src/genome-write.c:761:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(unsigned long long) currposition,(unsigned long long) currposition+strlen(segment)));
data/gmap-2020-11-20+ds/src/genome-write.c:762:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nbadchars = Compress_update_memory(nbadchars,genomecomp,segment,currposition,currposition+strlen(segment));
data/gmap-2020-11-20+ds/src/genome-write.c:763:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currposition += strlen(segment);
data/gmap-2020-11-20+ds/src/genome-write.c:796:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:796:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:797:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genome")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:797:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genome")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:813:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:813:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:814:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:814:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:828:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:828:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/genome-write.c:829:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome-write.c:829:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:183:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:183:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:183:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:184:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:184:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:187:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:187:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:187:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:188:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:194:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:194:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:194:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:195:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:195:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:198:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:198:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:198:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:199:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:216:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:216:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:216:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:217:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genome")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:244:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:244:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:244:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:245:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:245:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:248:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:248:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:248:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:249:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:255:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:255:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:255:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:256:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:256:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:259:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:259:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:259:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/genome.c:260:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:350:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->accession = (char *) MALLOC((strlen(accession)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/genome.c:404:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(this->fd,buffer,4);
data/gmap-2020-11-20+ds/src/genome.c:10763:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(segmentalt,segment,length);
data/gmap-2020-11-20+ds/src/genome.c:10818:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(segmentalt,segment,length);
data/gmap-2020-11-20+ds/src/get-genome.c:385:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:385:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:386:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altstrain.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:386:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altstrain.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1016:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1061:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) MALLOC((strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1061:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) MALLOC((strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1062:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".transcripts/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1062:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".transcripts/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1063:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(transcriptome_dbroot)+strlen(".align.iit")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1063:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(transcriptome_dbroot)+strlen(".align.iit")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1094:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1094:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1095:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1095:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1108:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
with_colon = (char *) CALLOC(strlen(chr)+strlen(":")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1108:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
with_colon = (char *) CALLOC(strlen(chr)+strlen(":")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1137:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(map_iitfile)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1142:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1142:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1143:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1143:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1149:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1149:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1150:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1150:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1174:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1174:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1175:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1175:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1234:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1234:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1235:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1235:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1258:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
with_colon = (char *) CALLOC(strlen(chr)+strlen(":")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1258:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
with_colon = (char *) CALLOC(strlen(chr)+strlen(":")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1292:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1292:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1293:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1293:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1309:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1309:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1310:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1310:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1316:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1316:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1317:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1317:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1338:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1338:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1339:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1339:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1384:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(string);
data/gmap-2020-11-20+ds/src/get-genome.c:1403:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(accession,line,p - line);
data/gmap-2020-11-20+ds/src/get-genome.c:1415:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(divstring,p,q - p);
data/gmap-2020-11-20+ds/src/get-genome.c:1437:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
annot_length += strlen(accession);
data/gmap-2020-11-20+ds/src/get-genome.c:1442:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
annot_length += strlen(space);
data/gmap-2020-11-20+ds/src/get-genome.c:1454:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(string);
data/gmap-2020-11-20+ds/src/get-genome.c:1470:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1470:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1471:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1471:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1477:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1477:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1478:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1478:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1588:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1588:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1589:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1589:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1595:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1595:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1596:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1596:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1752:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1752:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1753:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1753:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1759:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1759:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/get-genome.c:1760:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1760:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/get-genome.c:1803:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/get-genome.c:1803:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/get-genome.c:1803:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/get-genome.c:1804:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/getline.c:34:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(buffer);
data/gmap-2020-11-20+ds/src/getline.c:44:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length += strlen(ptr);
data/gmap-2020-11-20+ds/src/getline.c:71:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(buffer);
data/gmap-2020-11-20+ds/src/getline.c:81:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length += strlen(ptr);
data/gmap-2020-11-20+ds/src/getline.c:108:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(buffer);
data/gmap-2020-11-20+ds/src/getline.c:118:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length += strlen(ptr);
data/gmap-2020-11-20+ds/src/getline.c:146:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(buffer);
data/gmap-2020-11-20+ds/src/getline.c:156:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length += strlen(ptr);
data/gmap-2020-11-20+ds/src/getline.c:185:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(buffer);
data/gmap-2020-11-20+ds/src/getline.c:195:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length += strlen(ptr);
data/gmap-2020-11-20+ds/src/gmap.c:4781:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,Sequence_accession(queryseq),100);
data/gmap-2020-11-20+ds/src/gmap.c:4940:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,Sequence_accession(queryseq),100);
data/gmap-2020-11-20+ds/src/gmap.c:5004:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(lookup,typestring,destranded_len);
data/gmap-2020-11-20+ds/src/gmap.c:5010:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(lookup,typestring,destranded_len);
data/gmap-2020-11-20+ds/src/gmap.c:5582:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:5836:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
map_iitfile = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:5838:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((len = strlen(map_iitfile)) > 4 && strcmp(&(map_iitfile[len-4]),".iit") == 0) {
data/gmap-2020-11-20+ds/src/gmap.c:6011:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
inbuffer = Inbuffer_cmdline(/*queryseq*/p,/*querylength*/strlen(p),genome,genomealt);
data/gmap-2020-11-20+ds/src/gmap.c:6165:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6165:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6166:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6166:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6183:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6183:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6184:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6184:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6209:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6209:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6210:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6210:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6236:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6236:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6236:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap.c:6248:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6248:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmap.c:6249:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:130:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:130:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:130:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:144:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:144:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:144:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:158:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:158:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:158:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:172:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:172:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:172:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:186:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:186:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:186:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:200:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:200:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:200:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:214:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:214:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:214:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:228:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:228:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmap_select.c:228:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:240:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refstrain = (char *) CALLOC(strlen(strain)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:257:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refstrain = (char *) CALLOC(strlen("reference")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:283:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refstrain = (char *) CALLOC(strlen(strain)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:299:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refstrain = (char *) CALLOC(strlen("reference")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:389:16: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = getc(stdin)) == EOF || c == '>') {
data/gmap-2020-11-20+ds/src/gmapindex.c:405:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seglength += (Chrpos_T) strlen(Buffer);
data/gmap-2020-11-20+ds/src/gmapindex.c:430:12: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = getchar()) != EOF && c != '\n') {
data/gmap-2020-11-20+ds/src/gmapindex.c:435:12: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = getchar()) != EOF && c != '>') {
data/gmap-2020-11-20+ds/src/gmapindex.c:482:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(chr_string,chrpos_string,(coords-chrpos_string)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:539:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
typestring = (char *) CALLOC(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:609:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
primary_string = (char *) MALLOC((strlen(primary_chr)+10+2+10+1+1+10+2+10+1+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:615:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
altscaffold_info = (char *) CALLOC(strlen(primary_string)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:618:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
alt_scaffold_chr = (char *) CALLOC(strlen(chr_string)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:629:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
accession = (char *) CALLOC(strlen(accession_p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:720:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:720:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:721:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:721:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:732:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chrsubsetfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:732:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chrsubsetfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:733:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chrsubset")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:733:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chrsubset")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:820:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:820:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:821:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:821:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:886:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
primary_chr = (char *) MALLOC((strlen(altscaffold_info)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:906:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(primary_chr,p,q-p);
data/gmap-2020-11-20+ds/src/gmapindex.c:924:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string = (char *) MALLOC((strlen(primary_chr)+1+10+2+10+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:926:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
annot = (char *) CALLOC(strlen(string)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:952:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:952:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:953:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:953:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1057:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1057:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1058:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1058:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1120:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
annot = (char *) CALLOC(strlen(seglength)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1149:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1149:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1150:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1150:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1280:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) CALLOC(strlen(buffer)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1492:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
key = (char *) CALLOC(strlen(chrname_alt)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1496:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
key = (char *) CALLOC(strlen(chrname)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1512:9: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (getc(stdin) != '>') {
data/gmap-2020-11-20+ds/src/gmapindex.c:1577:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1577:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1578:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1578:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1615:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1615:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1616:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1616:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1625:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1625:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1626:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1626:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1666:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
source_genome = MALLOC((strlen(argv[i])+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1670:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1670:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1671:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1671:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1681:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1681:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1682:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1682:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1691:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1691:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1692:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1692:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".genomecomp")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1722:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1722:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1723:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1723:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1750:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1750:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1751:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1751:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1799:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1799:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1800:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1800:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1817:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_high = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1817:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_high = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1817:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_high = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1818:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1818:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1820:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(POSITIONS_HIGH_FILESUFFIX)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1824:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1824:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1824:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1825:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1825:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1827:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(POSITIONS_FILESUFFIX)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1836:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1836:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1836:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positionsfile_low = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1837:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1837:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/gmapindex.c:1839:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(POSITIONS_FILESUFFIX)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1880:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1880:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1881:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1881:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1911:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
source_genome = MALLOC((strlen(argv[i])+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1915:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1915:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chromosomefile = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1916:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1916:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1941:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1941:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
inputfiles[i] = (char *) CALLOC(strlen(argv[i])+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1942:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".refXXXregiondb")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1942:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".refXXXregiondb")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1956:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1956:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputfile = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gmapindex.c:1957:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".refXXXregiondb")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapindex.c:1957:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".refXXXregiondb")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:130:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:130:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:130:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:144:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:144:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:144:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:158:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:158:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:158:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:172:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:172:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:172:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:186:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:186:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:186:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:200:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:200:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:200:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:214:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:214:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:214:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:228:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:228:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gmapl_select.c:228:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:1211:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,Shortread_accession(queryseq1),100);
data/gmap-2020-11-20+ds/src/gsnap.c:1408:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,Shortread_accession(queryseq1),100);
data/gmap-2020-11-20+ds/src/gsnap.c:2812:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(transcriptomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2812:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(transcriptomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2813:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:2813:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:2838:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2838:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2839:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:2839:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:2856:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2856:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:2857:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:2857:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3011:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3011:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3012:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3056:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3056:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3057:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genes_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3083:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3083:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3083:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3094:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3094:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/gsnap.c:3095:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(splicing_file)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3173:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_tallydir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3173:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_tallydir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3173:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_tallydir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3183:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3183:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3183:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3211:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_runlengthdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3211:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_runlengthdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3211:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(user_runlengthdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3221:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3221:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap.c:3221:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:130:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:130:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:130:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:144:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:144:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:144:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:158:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:158:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:158:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:172:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:172:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:172:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:186:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:186:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:186:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:200:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:200:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:200:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:214:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:214:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:214:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:228:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:228:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnap_select.c:228:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:130:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:130:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:130:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512bw") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:144:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:144:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:144:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx512") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:158:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:158:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:158:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:172:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:172:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:172:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse42") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:186:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:186:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:186:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse41") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:200:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:200:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:200:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.ssse3") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:214:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:214:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:214:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse2") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:228:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:228:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/gsnapl_select.c:228:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.nosimd") + 1) * sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:623:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*restofheader)[1]),annotation,len);
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1386:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1390:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1394:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labels,new->label_length*sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1398:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1402:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotations,new->annot_length*sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1418:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1418:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1545:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:1545:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read-univ.c:2249:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string = (char *) CALLOC(strlen(chrstring)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:113:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:113:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:550:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*restofheader)[1]),annotation,len);
data/gmap-2020-11-20+ds/src/iit-read.c:716:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fieldvalue,p,fieldlen);
data/gmap-2020-11-20+ds/src/iit-read.c:1196:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strings[type] = (char *) CALLOC(strlen(typestring)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2482:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
data/gmap-2020-11-20+ds/src/iit-read.c:2486:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->values,new->value_length*sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2491:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
data/gmap-2020-11-20+ds/src/iit-read.c:2497:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
data/gmap-2020-11-20+ds/src/iit-read.c:2502:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read.c:2508:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read.c:2513:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->labels,new->label_length*sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2519:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
data/gmap-2020-11-20+ds/src/iit-read.c:2524:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read.c:2530:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
data/gmap-2020-11-20+ds/src/iit-read.c:2535:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(new->fd,new->annotations,new->annot_length*sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2556:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2556:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:2804:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->name = (char *) CALLOC(strlen(name)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:3061:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:3061:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:3081:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->name = (char *) CALLOC(strlen(name)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:3480:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:3480:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:6478:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) CALLOC(strlen(typestring)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit-read.c:6889:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*gene,annot,p - annot);
data/gmap-2020-11-20+ds/src/iit-write-univ.c:521:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(typestring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:529:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(typestring,strlen(typestring)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:559:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer8 += (UINT8) strlen(label)+1LU; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:562:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:566:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:576:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(label,strlen(label)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:599:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer8 += (UINT8) strlen(annot)+1LU; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:602:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:606:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write-univ.c:616:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(annot,strlen(annot)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:686:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(divstring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:700:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(divstring,strlen(divstring)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:760:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(divstring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:778:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
k += strlen(divstring);
data/gmap-2020-11-20+ds/src/iit-write.c:924:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(typestring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:940:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(typestring,strlen(typestring)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:956:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(fieldstring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:971:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(fieldstring,strlen(fieldstring)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1032:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer8 += (UINT8) strlen(label)+1LU; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1034:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1037:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1076:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(label,strlen(label)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1129:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer8 += (UINT8) strlen(annot)+1LU; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1131:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1134:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1173:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
FWRITE_CHARS(annot,strlen(annot)+1,fp); /* Write '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1243:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(typestring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1255:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
k += strlen(typestring);
data/gmap-2020-11-20+ds/src/iit-write.c:1270:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(fieldstring)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1282:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
k += strlen(fieldstring);
data/gmap-2020-11-20+ds/src/iit-write.c:1300:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
data/gmap-2020-11-20+ds/src/iit-write.c:1315:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
k += strlen(label);
data/gmap-2020-11-20+ds/src/iit-write.c:1646:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (strncpy(ptr,Buffer,strlen(Buffer)) == NULL) {
data/gmap-2020-11-20+ds/src/iit-write.c:1646:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strncpy(ptr,Buffer,strlen(Buffer)) == NULL) {
data/gmap-2020-11-20+ds/src/iit_get.c:215:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
annotlength = strlen(annotation);
data/gmap-2020-11-20+ds/src/iit_store.c:240:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) CALLOC(strlen(string)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:300:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*labellength = strlen(acc);
data/gmap-2020-11-20+ds/src/iit_store.c:313:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) MALLOC((strlen(divstring)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:333:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
divstring = (char *) MALLOC((strlen(p)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:339:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) MALLOC((strlen(divstring)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:376:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
valueptr += strlen("/value=");
data/gmap-2020-11-20+ds/src/iit_store.c:384:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
} else if (!strncmp(tag,"/value=",strlen("/value="))) {
data/gmap-2020-11-20+ds/src/iit_store.c:398:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*restofheader = (char *) MALLOC((strlen(p)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:406:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
typestring = (char *) MALLOC((strlen(tag)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:427:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*restofheader = (char *) MALLOC((strlen(p)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:462:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
valueptr += strlen("/value=");
data/gmap-2020-11-20+ds/src/iit_store.c:466:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*labellength = strlen(acc);
data/gmap-2020-11-20+ds/src/iit_store.c:484:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
} else if (!strncmp(p,"/value=",strlen("/value="))) {
data/gmap-2020-11-20+ds/src/iit_store.c:496:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
typestring = (char *) CALLOC(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:517:37: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (*firstchar = fgetc(fp)) != '>') {
data/gmap-2020-11-20+ds/src/iit_store.c:593:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
content_size += strlen(restofheader);
data/gmap-2020-11-20+ds/src/iit_store.c:664:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
content_size += strlen(restofheader);
data/gmap-2020-11-20+ds/src/iit_store.c:828:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
labelstr = (char *) CALLOC(strlen(labelid) + strlen("=") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:828:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
labelstr = (char *) CALLOC(strlen(labelid) + strlen("=") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:830:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
labelstrlen = strlen(labelstr);
data/gmap-2020-11-20+ds/src/iit_store.c:861:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
divstring = (char *) CALLOC(strlen(chr)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:890:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
label = (char *) MALLOC((strlen(Space)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:894:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
label = (char *) MALLOC((strlen(Space)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:897:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
label = (char *) MALLOC((strlen(idptr)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1037:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
typestring = (char *) MALLOC((strlen("circular")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1057:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
typestring = (char *) MALLOC((strlen("circular")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1151:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(outputfile) < 4) {
data/gmap-2020-11-20+ds/src/iit_store.c:1152:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(outputfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1152:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(outputfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1155:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = &(outputfile[strlen(outputfile)]);
data/gmap-2020-11-20+ds/src/iit_store.c:1158:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(outputfile)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1161:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(outputfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/iit_store.c:1161:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(outputfile)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:698:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
source_genome = MALLOC((strlen(argv[genomei])+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:702:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(argv[genomei])+strlen("/")+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:702:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(argv[genomei])+strlen("/")+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:703:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:703:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(source_dbroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:732:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
source_genome = MALLOC((strlen(argv[genomei])+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:759:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
source_genome = MALLOC((strlen(argv[genomei])+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:829:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pages_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:829:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pages_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:829:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pages_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:830:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:830:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:832:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64pages")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:837:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:837:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:837:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_pointers_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:838:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:838:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:840:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:844:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:844:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:844:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_offsets_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:845:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:845:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:847:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:852:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:852:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:852:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_high_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:853:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:853:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:855:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(POSITIONS_HIGH_FILESUFFIX)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-cat.c:860:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:860:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:860:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_positions_filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:861:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:861:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(IDX_FILESUFFIX)+
data/gmap-2020-11-20+ds/src/indexdb-cat.c:863:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(POSITIONS_FILESUFFIX)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-write.c:36:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/indexdb-write.c:759:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:759:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:759:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:760:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:760:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:762:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-write.c:771:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:771:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:771:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:772:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:772:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:774:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-write.c:1135:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pagesfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1135:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pagesfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1135:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pagesfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1136:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1136:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1138:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64pages")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-write.c:1147:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1147:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1147:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1148:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1148:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1150:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb-write.c:1159:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1159:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1159:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1160:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1160:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/indexdb-write.c:1162:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:37:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/indexdb.c:458:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsets_suffix = (char *) CALLOC(strlen("locoffsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:458:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsets_suffix = (char *) CALLOC(strlen("locoffsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:458:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsets_suffix = (char *) CALLOC(strlen("locoffsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:460:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_suffix = (char *) CALLOC(strlen("offsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:460:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_suffix = (char *) CALLOC(strlen("offsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:460:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_suffix = (char *) CALLOC(strlen("offsets")+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:462:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:462:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:462:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:464:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:464:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:464:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:477:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:477:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:477:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:479:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength = strlen(pattern);
data/gmap-2020-11-20+ds/src/indexdb.c:485:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = &(filename[strlen(pattern)]); /* Points after idx_filesuffix, e.g., "ref" */
data/gmap-2020-11-20+ds/src/indexdb.c:551:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:559:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:595:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:595:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:595:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:596:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_basename_ptr = &(offsets_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:596:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsets_basename_ptr = &(offsets_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:623:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:623:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:623:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:624:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_basename_ptr = &(positions_high_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:624:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_basename_ptr = &(positions_high_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:627:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:627:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:627:86: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:628:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_basename_ptr = &(positions_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:628:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_basename_ptr = &(positions_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:632:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_high_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:636:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:756:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_suffix = (char *) CALLOC(strlen("offsets32pages.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:756:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_suffix = (char *) CALLOC(strlen("offsets32pages.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:757:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_suffix = (char *) CALLOC(strlen("offsets32meta.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:757:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_suffix = (char *) CALLOC(strlen("offsets32meta.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:758:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsetsstrm_suffix = (char *) CALLOC(strlen("locoffsets32strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:758:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsetsstrm_suffix = (char *) CALLOC(strlen("locoffsets32strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:759:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_suffix = (char *) CALLOC(strlen("offsets32strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:759:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_suffix = (char *) CALLOC(strlen("offsets32strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:760:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:760:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:760:93: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:761:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:761:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:761:83: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:771:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_suffix = (char *) CALLOC(strlen("offsets64pages.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:771:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_suffix = (char *) CALLOC(strlen("offsets64pages.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:772:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_suffix = (char *) CALLOC(strlen("offsets64meta.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:772:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_suffix = (char *) CALLOC(strlen("offsets64meta.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:773:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsetsstrm_suffix = (char *) CALLOC(strlen("locoffsets64strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:773:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
locoffsetsstrm_suffix = (char *) CALLOC(strlen("locoffsets64strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:774:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_suffix = (char *) CALLOC(strlen("offsets64strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:774:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_suffix = (char *) CALLOC(strlen("offsets64strm.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:775:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:775:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:775:93: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_suffix = (char *) CALLOC(strlen(POSITIONS_HIGH_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:776:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:776:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:776:83: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_suffix = (char *) CALLOC(strlen(POSITIONS_FILESUFFIX)+strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:807:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern1 = (char *) CALLOC(strlen(fileroot)+strlen(".")+1,sizeof(char)); /* e.g., "hg19." */
data/gmap-2020-11-20+ds/src/indexdb.c:807:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern1 = (char *) CALLOC(strlen(fileroot)+strlen(".")+1,sizeof(char)); /* e.g., "hg19." */
data/gmap-2020-11-20+ds/src/indexdb.c:809:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength1 = strlen(pattern1);
data/gmap-2020-11-20+ds/src/indexdb.c:811:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern2 = (char *) CALLOC(strlen(".")+strlen(idx_filesuffix)+1,sizeof(char)); /* e.g., ".pr" */
data/gmap-2020-11-20+ds/src/indexdb.c:811:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern2 = (char *) CALLOC(strlen(".")+strlen(idx_filesuffix)+1,sizeof(char)); /* e.g., ".pr" */
data/gmap-2020-11-20+ds/src/indexdb.c:813:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength2 = strlen(pattern2);
data/gmap-2020-11-20+ds/src/indexdb.c:819:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
a = &(filename[strlen(pattern1)]); /* Points after fileroot, e.g., "hg19." */
data/gmap-2020-11-20+ds/src/indexdb.c:885:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:899:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:899:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:899:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:901:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength = strlen(pattern);
data/gmap-2020-11-20+ds/src/indexdb.c:907:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = &(filename[strlen(pattern)]); /* Points after idx_filesuffix, e.g., "ref" */
data/gmap-2020-11-20+ds/src/indexdb.c:952:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:986:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:986:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:986:77: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:987:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_basename_ptr = &(offsetsstrm_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:987:76: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsstrm_basename_ptr = &(offsetsstrm_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1016:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetsmeta_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1016:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetsmeta_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1016:88: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetsmeta_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1017:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_basename_ptr = &(offsetsmeta_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1017:76: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsmeta_basename_ptr = &(offsetsmeta_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1021:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(offsetsmeta_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:1040:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetspages_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1040:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetspages_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1040:89: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetspages_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1041:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_basename_ptr = &(offsetspages_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1041:78: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetspages_basename_ptr = &(offsetspages_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1045:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(offsetspages_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:1053:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1053:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1053:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_high_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1054:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_basename_ptr = &(positions_high_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1054:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_high_basename_ptr = &(positions_high_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1057:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1057:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1057:86: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(positions_suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/indexdb.c:1058:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_basename_ptr = &(positions_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1058:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
positions_basename_ptr = &(positions_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/indexdb.c:1062:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_high_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:1066:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_basename_ptr,base_filename,rootlength);
data/gmap-2020-11-20+ds/src/indexdb.c:1074:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_high_basename_ptr,base_filename,rootlength-BASE_KMER_SAMPLING); /* e.g., skip "153" */
data/gmap-2020-11-20+ds/src/indexdb.c:1075:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(positions_high_basename_ptr[rootlength-BASE_KMER_SAMPLING]),&(base_filename[rootlength-BASE_KMER_SAMPLING]),BASE_KMER_SAMPLING);
data/gmap-2020-11-20+ds/src/indexdb.c:1079:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(positions_basename_ptr,base_filename,rootlength-BASE_KMER_SAMPLING); /* e.g., skip "153" */
data/gmap-2020-11-20+ds/src/indexdb.c:1080:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(positions_basename_ptr[rootlength-BASE_KMER_SAMPLING]),&(base_filename[rootlength-BASE_KMER_SAMPLING]),BASE_KMER_SAMPLING);
data/gmap-2020-11-20+ds/src/indexdb.c:1838:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/indexdb.c:1862:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_high_fd,buffer,1);
data/gmap-2020-11-20+ds/src/indexdb.c:1866:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/indexdb.c:1879:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_high_fd,buffer,1);
data/gmap-2020-11-20+ds/src/indexdb.c:1883:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/indexdb.c:1921:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/indexdb.c:1935:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/indexdb.c:1963:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(positions_fd,buffer,4);
data/gmap-2020-11-20+ds/src/intlist.c:445:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/intlist.c:448:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/list.c:439:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(substring,p,substringlen);
data/gmap-2020-11-20+ds/src/list.c:449:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(substring,p,substringlen);
data/gmap-2020-11-20+ds/src/outbuffer.c:170:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOC((strlen(failedinput_root)+strlen(".1")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/outbuffer.c:170:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOC((strlen(failedinput_root)+strlen(".1")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/outbuffer.c:195:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOC((strlen(failedinput_root)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/pair.c:594:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
while (i + (int) strlen(RULER) < length) {
data/gmap-2020-11-20+ds/src/pair.c:596:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i += (int) strlen(RULER);
data/gmap-2020-11-20+ds/src/pair.c:819:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
margin = (int) strlen(Buffer) + 1;
data/gmap-2020-11-20+ds/src/pair.c:826:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((int) strlen(Buffer) + 1 > margin) {
data/gmap-2020-11-20+ds/src/pair.c:827:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
margin = (int) strlen(Buffer) + 1;
data/gmap-2020-11-20+ds/src/pair.c:943:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
margin = (space - strlen(cdnabreak))/2;
data/gmap-2020-11-20+ds/src/pair.c:949:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (k = 0; k < (int) strlen(cdnabreak); k++) {
data/gmap-2020-11-20+ds/src/pair.c:954:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
margin = (space - strlen(genomicbreak))/2;
data/gmap-2020-11-20+ds/src/pair.c:960:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (k = 0; k < (int) strlen(genomicbreak); k++) {
data/gmap-2020-11-20+ds/src/pair.c:972:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
margin = (space - strlen(intronstring))/2;
data/gmap-2020-11-20+ds/src/pair.c:978:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (k = 0; k < (int) strlen(intronstring); k++) {
data/gmap-2020-11-20+ds/src/pair.c:2397:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_token = (char *) MALLOC_OUT((strlen(old_token)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/pair.c:2436:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) MALLOC_OUT((strlen(token)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/pair.c:5021:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = curr_token[strlen(curr_token)-1];
data/gmap-2020-11-20+ds/src/pair.c:5072:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = curr_token[strlen(curr_token)-1];
data/gmap-2020-11-20+ds/src/pair.c:5105:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = token[strlen(token)-1];
data/gmap-2020-11-20+ds/src/pair.c:5961:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = cigar_token[strlen(cigar_token)-1];
data/gmap-2020-11-20+ds/src/pair.c:6056:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = cigar_token[strlen(cigar_token)-1];
data/gmap-2020-11-20+ds/src/parserange.c:81:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) MALLOCA((strlen(string)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:254:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:254:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:254:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:255:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".chromosome.iit")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:298:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*divstring,query,(coords-query)*sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:391:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*div,query,(coords-query)*sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:405:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:405:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:405:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:406:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".chromosome.iit")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:450:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:450:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:450:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:451:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".contig.iit")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:505:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:505:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:505:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:506:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".contig.iit")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:522:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:522:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:522:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/parserange.c:523:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".chromosome.iit")+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:563:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*div,query,(coords-query)*sizeof(char));
data/gmap-2020-11-20+ds/src/parserange.c:695:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*div,query,(coords-query)*sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb-write.c:37:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/regiondb-write.c:146:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regionfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/regiondb-write.c:146:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regionfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/regiondb-write.c:146:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regionfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/regiondb-write.c:147:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/regiondb-write.c:147:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(filesuffix)+
data/gmap-2020-11-20+ds/src/regiondb-write.c:149:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen("regiondb")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:36:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/regiondb.c:1515:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_suffix = (char *) CALLOC(strlen("regiondb.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1515:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_suffix = (char *) CALLOC(strlen("regiondb.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1533:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern1 = (char *) CALLOC(strlen(fileroot)+strlen(".")+1,sizeof(char)); /* e.g., "hg19." */
data/gmap-2020-11-20+ds/src/regiondb.c:1533:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern1 = (char *) CALLOC(strlen(fileroot)+strlen(".")+1,sizeof(char)); /* e.g., "hg19." */
data/gmap-2020-11-20+ds/src/regiondb.c:1535:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength1 = strlen(pattern1);
data/gmap-2020-11-20+ds/src/regiondb.c:1537:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern2 = (char *) CALLOC(strlen(".")+strlen(idx_filesuffix)+1,sizeof(char)); /* e.g., ".pr" */
data/gmap-2020-11-20+ds/src/regiondb.c:1537:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern2 = (char *) CALLOC(strlen(".")+strlen(idx_filesuffix)+1,sizeof(char)); /* e.g., ".pr" */
data/gmap-2020-11-20+ds/src/regiondb.c:1539:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength2 = strlen(pattern2);
data/gmap-2020-11-20+ds/src/regiondb.c:1545:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
a = &(filename[strlen(pattern1)]); /* Points after fileroot, e.g., "hg19." */
data/gmap-2020-11-20+ds/src/regiondb.c:1604:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1618:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1618:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1618:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pattern = (char *) CALLOC(strlen(fileroot)+strlen(".")+strlen(idx_filesuffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1620:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
patternlength = strlen(pattern);
data/gmap-2020-11-20+ds/src/regiondb.c:1626:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = &(filename[strlen(pattern)]); /* Points after idx_filesuffix, e.g., "ref" */
data/gmap-2020-11-20+ds/src/regiondb.c:1663:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
base_filename = (char *) CALLOC(strlen(filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1692:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1692:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1692:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/regiondb.c:1693:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_basename_ptr = &(regiondb_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/regiondb.c:1693:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
regiondb_basename_ptr = &(regiondb_filename[strlen(genomesubdir)+strlen("/")]);
data/gmap-2020-11-20+ds/src/sam_sort.c:907:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
linelength = strlen(line);
data/gmap-2020-11-20+ds/src/sam_sort.c:911:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(ptr,p,allowed);
data/gmap-2020-11-20+ds/src/sam_sort.c:1227:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char *read;
data/gmap-2020-11-20+ds/src/sam_sort.c:1240:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,this->linelen);
data/gmap-2020-11-20+ds/src/sam_sort.c:1243:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/sam_sort.c:1245:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->queryseq5 = read;
data/gmap-2020-11-20+ds/src/sam_sort.c:1246:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
debug9(printf("queryseq5 is %s\n",read));
data/gmap-2020-11-20+ds/src/sam_sort.c:1255:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
data/gmap-2020-11-20+ds/src/sam_sort.c:1258:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/sam_sort.c:1260:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->queryseq3 = read;
data/gmap-2020-11-20+ds/src/sam_sort.c:1261:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
debug9(printf("queryseq3 is %s\n",read));
data/gmap-2020-11-20+ds/src/sam_sort.c:1268:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,this->linelen);
data/gmap-2020-11-20+ds/src/sam_sort.c:1271:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/sam_sort.c:1273:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->queryseq3 = read;
data/gmap-2020-11-20+ds/src/sam_sort.c:1274:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
debug9(printf("queryseq3 is %s\n",read));
data/gmap-2020-11-20+ds/src/sam_sort.c:1283:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Samread_parse_read_fromfile(fp_sam,&flag,&readlength,&read,mate->linelen);
data/gmap-2020-11-20+ds/src/sam_sort.c:1286:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/sam_sort.c:1288:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->queryseq5 = read;
data/gmap-2020-11-20+ds/src/sam_sort.c:1289:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
debug9(printf("queryseq5 is %s\n",read));
data/gmap-2020-11-20+ds/src/sam_sort.c:1955:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/sam_sort.c:1975:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/sam_sort.c:1975:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/sam_sort.c:1976:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/sam_sort.c:1976:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/sam_sort.c:2046:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
linelen += strlen(lastp);
data/gmap-2020-11-20+ds/src/samheader.c:29:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(split_output_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/samheader.c:85:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(split_output_root)+strlen(".")+strlen(suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/samheader.c:85:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(split_output_root)+strlen(".")+strlen(suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/samheader.c:85:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(split_output_root)+strlen(".")+strlen(suffix)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/samheader.c:115:32: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (headerlen > 0 && (c = fgetc(input)) != '\t') {
data/gmap-2020-11-20+ds/src/samheader.c:125:32: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (headerlen > 0 && (c = fgetc(input)) != '\t') {
data/gmap-2020-11-20+ds/src/samheader.c:136:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c0 = fgetc(input);
data/gmap-2020-11-20+ds/src/samheader.c:137:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c1 = fgetc(input);
data/gmap-2020-11-20+ds/src/samheader.c:138:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c2 = fgetc(input);
data/gmap-2020-11-20+ds/src/samheader.c:144:31: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (headerlen > 0 && fgetc(input) != '\n') {
data/gmap-2020-11-20+ds/src/samheader.c:223:28: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (c = getc(fp)) == '@') {
data/gmap-2020-11-20+ds/src/samheader.c:225:30: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (c = getc(fp)) != '\n') {
data/gmap-2020-11-20+ds/src/samread.c:445:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char *substring, *read, *clipped;
data/gmap-2020-11-20+ds/src/samread.c:461:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,line,*acclength);
data/gmap-2020-11-20+ds/src/samread.c:578:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = read;
data/gmap-2020-11-20+ds/src/samread.c:581:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*readlength = (p - read)/sizeof(char);
data/gmap-2020-11-20+ds/src/samread.c:590:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = read;
data/gmap-2020-11-20+ds/src/samread.c:593:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
subseq_length = (p - read)/sizeof(char);
data/gmap-2020-11-20+ds/src/samread.c:608:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[hardclip_low]);
data/gmap-2020-11-20+ds/src/samread.c:630:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[0]);
data/gmap-2020-11-20+ds/src/samread.c:636:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[(*readlength) - hardclip_high]);
data/gmap-2020-11-20+ds/src/samread.c:645:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read[*readlength] = '\0';
data/gmap-2020-11-20+ds/src/samread.c:649:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,*readlength);
data/gmap-2020-11-20+ds/src/samread.c:652:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*hashseq = string_hash(read);
data/gmap-2020-11-20+ds/src/samread.c:666:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int *readlength, char **read, char **quality_string, char *line) {
data/gmap-2020-11-20+ds/src/samread.c:676:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*acc,line,length);
data/gmap-2020-11-20+ds/src/samread.c:701:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr,p,length);
data/gmap-2020-11-20+ds/src/samread.c:749:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*cigar,p,length);
data/gmap-2020-11-20+ds/src/samread.c:764:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*mate_chr,p,length);
data/gmap-2020-11-20+ds/src/samread.c:810:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*read,p,*readlength);
data/gmap-2020-11-20+ds/src/samread.c:810:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
strncpy(*read,p,*readlength);
data/gmap-2020-11-20+ds/src/samread.c:811:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(*read)[*readlength] = '\0';
data/gmap-2020-11-20+ds/src/samread.c:813:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
debug(printf(" read = %s\n",*read));
data/gmap-2020-11-20+ds/src/samread.c:820:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*quality_string,p,length);
data/gmap-2020-11-20+ds/src/samread.c:845:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c0 = fgetc(fp);
data/gmap-2020-11-20+ds/src/samread.c:846:10: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c1 = fgetc(fp);
data/gmap-2020-11-20+ds/src/samread.c:849:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fgetc(fp); /* : */
data/gmap-2020-11-20+ds/src/samread.c:850:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fgetc(fp); /* type */
data/gmap-2020-11-20+ds/src/samread.c:851:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fgetc(fp); /* : */
data/gmap-2020-11-20+ds/src/samread.c:853:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = *p++ = fgetc(fp)) != EOF && c != '\n' && c != '\t') ;
data/gmap-2020-11-20+ds/src/samread.c:857:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(fp)) != EOF && c != '\n' && c != '\t') ;
data/gmap-2020-11-20+ds/src/samread.c:867:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char *read;
data/gmap-2020-11-20+ds/src/samread.c:928:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[hardclip_low]);
data/gmap-2020-11-20+ds/src/samread.c:941:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[0]);
data/gmap-2020-11-20+ds/src/samread.c:947:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[readlength - hardclip_high]);
data/gmap-2020-11-20+ds/src/samread.c:958:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read[readlength] = '\0';
data/gmap-2020-11-20+ds/src/samread.c:961:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/samread.c:966:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return read;
data/gmap-2020-11-20+ds/src/samread.c:972:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char *read;
data/gmap-2020-11-20+ds/src/samread.c:1033:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[hardclip_low]);
data/gmap-2020-11-20+ds/src/samread.c:1046:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[0]);
data/gmap-2020-11-20+ds/src/samread.c:1052:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p = &(read[readlength - hardclip_high]);
data/gmap-2020-11-20+ds/src/samread.c:1063:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read[readlength] = '\0';
data/gmap-2020-11-20+ds/src/samread.c:1066:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
make_complement_inplace(read,readlength);
data/gmap-2020-11-20+ds/src/samread.c:1071:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return read;
data/gmap-2020-11-20+ds/src/samread.c:1092:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*acc,line,length);
data/gmap-2020-11-20+ds/src/samread.c:1118:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(chr,p,length);
data/gmap-2020-11-20+ds/src/samread.c:1165:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*cigar,p,length);
data/gmap-2020-11-20+ds/src/samread.c:1185:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
flag_strlen = strlen(flag_string);
data/gmap-2020-11-20+ds/src/samread.c:1187:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newflag_strlen = strlen(newflag_string);
data/gmap-2020-11-20+ds/src/sequence.c:124:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
header = MALLOC(strlen("Annot=\"")+(strlen(p)+strlen("\"")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:124:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
header = MALLOC(strlen("Annot=\"")+(strlen(p)+strlen("\"")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:124:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
header = MALLOC(strlen("Annot=\"")+(strlen(p)+strlen("\"")+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:139:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
q = header = MALLOC((strlen(p)+1)*sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:487:33: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (okayp == false && (c = fgetc(fp)) != EOF) {
data/gmap-2020-11-20+ds/src/sequence.c:564:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
this->acc = (char *) CALLOC_IN(strlen("NO_HEADER")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:613:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
this->restofheader = (char *) CALLOC_IN(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/sequence.c:739:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = fgetc(fp)) == EOF || (init_char_p == false && (c == '@' || c == '>' || c == '<' || c == '+'))) {
data/gmap-2020-11-20+ds/src/sequence.c:763:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/sequence.c:780:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/sequence.c:796:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptr += strlen(ptr);
data/gmap-2020-11-20+ds/src/sequence.c:839:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = fgetc(fp)) == EOF || (init_char_p == false && (c == '@' || c == '>' || c == '<' || c == '+'))) {
data/gmap-2020-11-20+ds/src/sequence.c:861:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/sequence.c:877:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/sequence.c:893:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptr += strlen(ptr);
data/gmap-2020-11-20+ds/src/sequence.c:990:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(copy,contents,length);
data/gmap-2020-11-20+ds/src/sequence.c:1398:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->contents,pointer1,length1);
data/gmap-2020-11-20+ds/src/sequence.c:1402:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(new->contents[length1]),pointer2a,length2a);
data/gmap-2020-11-20+ds/src/sequence.c:1407:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(new->contents[length1+length2a]),pointer2b,length2b);
data/gmap-2020-11-20+ds/src/sequence.c:1426:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(input);
data/gmap-2020-11-20+ds/src/sequence.c:1436:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->quality,pointer1,length1);
data/gmap-2020-11-20+ds/src/sequence.c:1440:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(new->quality[length1]),pointer2a,length2a);
data/gmap-2020-11-20+ds/src/sequence.c:1444:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(new->quality[length1+length2a]),pointer2b,length2b);
data/gmap-2020-11-20+ds/src/shortread.c:242:33: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (okayp == false && (c = fgetc(fp)) != EOF) {
data/gmap-2020-11-20+ds/src/shortread.c:367:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:381:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:420:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*restofheader = (char *) CALLOC_IN(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:493:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*restofheader = (char *) CALLOC_IN(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:567:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*restofheader = (char *) CALLOC_IN(strlen(p)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:665:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:679:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:923:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:930:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:1073:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nchars += strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:1081:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:1112:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((*nextchar = fgetc(fp)) != EOF && *nextchar != '\n') {
data/gmap-2020-11-20+ds/src/shortread.c:1118:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(fp);
data/gmap-2020-11-20+ds/src/shortread.c:1131:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptr += strlen(ptr);
data/gmap-2020-11-20+ds/src/shortread.c:1134:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(fp);
data/gmap-2020-11-20+ds/src/shortread.c:1178:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:1224:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptr += strlen(ptr);
data/gmap-2020-11-20+ds/src/shortread.c:1270:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlenp = strlen(p);
data/gmap-2020-11-20+ds/src/shortread.c:1316:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ptr += strlen(ptr);
data/gmap-2020-11-20+ds/src/shortread.c:1842:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq1->chop,&(queryseq1->contents[queryseq1->fulllength - chop1]),chop1);
data/gmap-2020-11-20+ds/src/shortread.c:1848:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq1->chop_quality,&(queryseq1->quality[queryseq1->fulllength - chop1]),chop1);
data/gmap-2020-11-20+ds/src/shortread.c:1858:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq2->chop,queryseq2->contents,chop2);
data/gmap-2020-11-20+ds/src/shortread.c:1866:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq2->chop_quality,queryseq2->quality,chop2);
data/gmap-2020-11-20+ds/src/shortread.c:1942:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq1->chop,&(queryseq1->contents[fulllength1]),chop1);
data/gmap-2020-11-20+ds/src/shortread.c:1950:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq1->chop_quality,&(queryseq1->quality[fulllength1]),chop1);
data/gmap-2020-11-20+ds/src/shortread.c:1962:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq2->chop,queryseq2->contents,chop2);
data/gmap-2020-11-20+ds/src/shortread.c:1970:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(queryseq2->chop_quality,queryseq2->quality,chop2);
data/gmap-2020-11-20+ds/src/shortread.c:2148:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->acc = (char *) CALLOC_IN(strlen(acc)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:2157:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->restofheader = (char *) CALLOC_IN(strlen(restofheader)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/shortread.c:2171:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->barcode,&(sequence[0]),barcode_length);
data/gmap-2020-11-20+ds/src/shortread.c:2180:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->endtrim,&(sequence[sequence_length - endtrim_length]),endtrim_length);
data/gmap-2020-11-20+ds/src/shortread.c:2210:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->contents,sequence,sequence_length);
data/gmap-2020-11-20+ds/src/shortread.c:2219:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new->quality,quality,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:2320:29: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if ((*nextchar = fgetc(*input1)) == '\r' || *nextchar == '\n') {
data/gmap-2020-11-20+ds/src/shortread.c:2322:48: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (*nextchar != EOF && ((*nextchar = fgetc(*input1)) != '>')) {
data/gmap-2020-11-20+ds/src/shortread.c:2344:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(*input1);
data/gmap-2020-11-20+ds/src/shortread.c:2400:28: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if ((nextchar2 = fgetc(*input2)) == '\r' || nextchar2 == '\n') {
data/gmap-2020-11-20+ds/src/shortread.c:2402:47: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (nextchar2 != EOF && ((nextchar2 = fgetc(*input2)) != '>')) {
data/gmap-2020-11-20+ds/src/shortread.c:2421:20: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(*input1);
data/gmap-2020-11-20+ds/src/shortread.c:2444:20: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nextchar2 = fgetc(*input2);
data/gmap-2020-11-20+ds/src/shortread.c:2479:18: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(*input1);
data/gmap-2020-11-20+ds/src/shortread.c:3057:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,line,length);
data/gmap-2020-11-20+ds/src/shortread.c:3072:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_1,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3089:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3108:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_2,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3124:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3178:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,line,length);
data/gmap-2020-11-20+ds/src/shortread.c:3193:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_1,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3210:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3229:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_2,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3245:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3296:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(acc,line,length);
data/gmap-2020-11-20+ds/src/shortread.c:3311:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_1,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3328:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3347:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_read_2,q,fulllength);
data/gmap-2020-11-20+ds/src/shortread.c:3363:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(long_quality,q,quality_length);
data/gmap-2020-11-20+ds/src/shortread.c:3468:19: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(*input1);
data/gmap-2020-11-20+ds/src/shortread.c:3485:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*nextchar = fgetc(*input1);
data/gmap-2020-11-20+ds/src/shortread.c:3528:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nextchar2 = fgetc(*input2);
data/gmap-2020-11-20+ds/src/shortread.c:3545:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nextchar2 = fgetc(*input2);
data/gmap-2020-11-20+ds/src/simplepair.c:381:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
copy = (char *) MALLOC_OUT((strlen(token)+1) * sizeof(char));
data/gmap-2020-11-20+ds/src/simplepair.c:423:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = token[strlen(token)-1];
data/gmap-2020-11-20+ds/src/simplepair.c:445:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = curr_token[strlen(curr_token)-1];
data/gmap-2020-11-20+ds/src/simplepair.c:496:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = curr_token[strlen(curr_token)-1];
data/gmap-2020-11-20+ds/src/simplepair.c:1161:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = cigar_token[strlen(cigar_token)-1];
data/gmap-2020-11-20+ds/src/simplepair.c:1256:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
type = cigar_token[strlen(cigar_token)-1];
data/gmap-2020-11-20+ds/src/snpindex.c:33:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/snpindex.c:359:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(snptype) != 2) {
data/gmap-2020-11-20+ds/src/snpindex.c:1299:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1299:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1300:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1300:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1321:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1321:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1322:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1322:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1380:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsmetafile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->pointers_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1380:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsmetafile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->pointers_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1380:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsmetafile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->pointers_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1381:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1381:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1383:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsstrmfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->offsets_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1383:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsstrmfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->offsets_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1383:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snp_offsetsstrmfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->offsets_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1384:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1384:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1387:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snponly_offsetsmetafile = (char *) CALLOC(strlen(snp_offsetsmetafile) + strlen(".only") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1387:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snponly_offsetsmetafile = (char *) CALLOC(strlen(snp_offsetsmetafile) + strlen(".only") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1389:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snponly_offsetsstrmfile = (char *) CALLOC(strlen(snp_offsetsstrmfile) + strlen(".only") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1389:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snponly_offsetsstrmfile = (char *) CALLOC(strlen(snp_offsetsstrmfile) + strlen(".only") + 1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1400:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1400:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1400:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1401:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1401:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1421:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1421:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1421:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
data/gmap-2020-11-20+ds/src/snpindex.c:1422:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1422:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".genomebits128.")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1500:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_high_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1500:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_high_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1500:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_high_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1501:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1501:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1510:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1510:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1510:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(indexdb_filenames->positions_basename_ptr)+
data/gmap-2020-11-20+ds/src/snpindex.c:1511:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1511:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(".")+strlen(snps_root)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1614:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename1 = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1614:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename1 = (char *) CALLOC(strlen(mapdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1615:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1615:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1626:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+ strlen(fileroot) + strlen(".maps/") +
data/gmap-2020-11-20+ds/src/snpindex.c:1626:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+ strlen(fileroot) + strlen(".maps/") +
data/gmap-2020-11-20+ds/src/snpindex.c:1626:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+ strlen(fileroot) + strlen(".maps/") +
data/gmap-2020-11-20+ds/src/snpindex.c:1626:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+ strlen(fileroot) + strlen(".maps/") +
data/gmap-2020-11-20+ds/src/snpindex.c:1627:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1627:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1630:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1630:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/snpindex.c:1631:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/snpindex.c:1631:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(snps_root)+strlen(".iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/stage2.c:467:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo,&(queryseq_ptr[i]),indexsize);
data/gmap-2020-11-20+ds/src/stage2.c:501:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo,&(queryseq_ptr[i]),indexsize);
data/gmap-2020-11-20+ds/src/stage2.c:3892:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug9(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage2.c:3910:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug9(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage2.c:4197:12: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug0(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage2.c:4285:12: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug0(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage2.c:4766:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug9(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage2.c:4782:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
debug9(strncpy(oligo,&(queryseq_ptr[curr_querypos]),indexsize));
data/gmap-2020-11-20+ds/src/stage3hr.c:10621:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*queryseq_merged,queryseq_ptr_5,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10622:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_3[querylength3 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10629:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*quality_merged,quality_ptr_5,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10630:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_3[querylength3 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10663:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*queryseq_merged,queryseq_ptr_3,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10664:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_5[querylength5 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10671:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*quality_merged,quality_ptr_3,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10672:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_5[querylength5 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10708:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*queryseq_merged,queryseq_ptr_3,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10709:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_5[querylength5 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10716:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*quality_merged,quality_ptr_3,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10717:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_5[querylength5 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10748:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*queryseq_merged,queryseq_ptr_5,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10749:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*queryseq_merged)[querylengthA]),&(queryseq_ptr_3[querylength3 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/stage3hr.c:10756:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*quality_merged,quality_ptr_5,querylengthA);
data/gmap-2020-11-20+ds/src/stage3hr.c:10757:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&((*quality_merged)[querylengthA]),&(quality_ptr_3[querylength3 - querylengthB]),querylengthB);
data/gmap-2020-11-20+ds/src/substring.c:918:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(result[querystart]),&(genomic_diff[querystart]),queryend-querystart);
data/gmap-2020-11-20+ds/src/substring.c:1003:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(&(result[start]),&(genomic_diff[start]),end-start);
data/gmap-2020-11-20+ds/src/substring.c:3768:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
assert((int) strlen(old->genomic_bothdiff) == old->querylength);
data/gmap-2020-11-20+ds/src/substring.c:3769:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->genomic_bothdiff = (char *) CALLOC_OUT(strlen(old->genomic_bothdiff)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/substring.c:3774:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
assert((int) strlen(old->genomic_bothdiff) == old->querylength);
data/gmap-2020-11-20+ds/src/substring.c:3775:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
assert((int) strlen(old->genomic_refdiff) == old->querylength);
data/gmap-2020-11-20+ds/src/substring.c:3776:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->genomic_bothdiff = (char *) CALLOC_OUT(strlen(old->genomic_bothdiff)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/substring.c:3778:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new->genomic_refdiff = (char *) CALLOC_OUT(strlen(old->genomic_refdiff)+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:114:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/transcriptome.c:114:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/transcriptome.c:115:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/transcriptome.c:115:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/transcriptome.c:115:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/transcriptome.c:119:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".chrnums")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:119:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".chrnums")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:138:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:138:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:155:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:155:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:173:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".exoninfo")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/transcriptome.c:173:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".exoninfo")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:31:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define NAMLEN(dirent) strlen((dirent)->d_name)
data/gmap-2020-11-20+ds/src/trindex.c:176:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:176:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:177:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/trindex.c:177:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/trindex.c:177:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".transcripts/")+strlen(transcriptome_fileroot)+1,
data/gmap-2020-11-20+ds/src/trindex.c:197:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".align.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:197:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".align.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:202:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((nread = read(in,buf,BUF_SIZE)) > 0) {
data/gmap-2020-11-20+ds/src/trindex.c:216:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:216:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:217:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:217:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(genome_fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:226:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(transcriptomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:226:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iitfile = (char *) CALLOC(strlen(transcriptomesubdir)+strlen("/")+
data/gmap-2020-11-20+ds/src/trindex.c:227:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(transcriptome_fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:227:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(transcriptome_fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:244:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".exoninfo")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:244:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".exoninfo")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:283:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".chrnums")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:283:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = (char *) CALLOC(strlen(info_root)+strlen(".chrnums")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:294:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(info_root)+strlen(".offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:294:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pointersfile = (char *) CALLOC(strlen(info_root)+strlen(".offsets64meta")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:297:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(info_root)+strlen(".offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/trindex.c:297:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offsetsfile = (char *) CALLOC(strlen(info_root)+strlen(".offsets64strm")+1,sizeof(char));
data/gmap-2020-11-20+ds/src/uint8list.c:283:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:286:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:315:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uint8list.c:318:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:284:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:287:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:316:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
data/gmap-2020-11-20+ds/src/uintlist.c:319:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlength += strlen(Buffer);
ANALYSIS SUMMARY:
Hits = 2993
Lines analyzed = 528756 in approximately 23.40 seconds (22601 lines/second)
Physical Source Lines of Code (SLOC) = 459193
Hits@level = [0] 15570 [1] 1362 [2] 1147 [3] 20 [4] 464 [5] 0
Hits@level+ = [0+] 18563 [1+] 2993 [2+] 1631 [3+] 484 [4+] 464 [5+] 0
Hits/KSLOC@level+ = [0+] 40.4253 [1+] 6.51796 [2+] 3.55188 [3+] 1.05402 [4+] 1.01047 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.