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/exonerate-2.4.0/src/struct/fsm.test.c
Examining data/exonerate-2.4.0/src/struct/fsm.c
Examining data/exonerate-2.4.0/src/struct/matrix.test.c
Examining data/exonerate-2.4.0/src/struct/matrix.c
Examining data/exonerate-2.4.0/src/struct/pqueue.test.c
Examining data/exonerate-2.4.0/src/struct/pqueue.c
Examining data/exonerate-2.4.0/src/struct/recyclebin.c
Examining data/exonerate-2.4.0/src/struct/slist.test.c
Examining data/exonerate-2.4.0/src/struct/slist.c
Examining data/exonerate-2.4.0/src/struct/rangetree.test.c
Examining data/exonerate-2.4.0/src/struct/rangetree.c
Examining data/exonerate-2.4.0/src/struct/vfsm.test.c
Examining data/exonerate-2.4.0/src/struct/vfsm.c
Examining data/exonerate-2.4.0/src/struct/recyclebin.test.c
Examining data/exonerate-2.4.0/src/struct/sparsecache.test.c
Examining data/exonerate-2.4.0/src/struct/sparsecache.c
Examining data/exonerate-2.4.0/src/struct/dejavu.test.c
Examining data/exonerate-2.4.0/src/struct/dejavu.c
Examining data/exonerate-2.4.0/src/struct/bitarray.test.c
Examining data/exonerate-2.4.0/src/struct/bitarray.c
Examining data/exonerate-2.4.0/src/struct/splaytree.test.c
Examining data/exonerate-2.4.0/src/struct/splaytree.c
Examining data/exonerate-2.4.0/src/struct/noitree.test.c
Examining data/exonerate-2.4.0/src/struct/noitree.c
Examining data/exonerate-2.4.0/src/struct/fsm.h
Examining data/exonerate-2.4.0/src/struct/matrix.h
Examining data/exonerate-2.4.0/src/struct/pqueue.h
Examining data/exonerate-2.4.0/src/struct/slist.h
Examining data/exonerate-2.4.0/src/struct/rangetree.h
Examining data/exonerate-2.4.0/src/struct/vfsm.h
Examining data/exonerate-2.4.0/src/struct/recyclebin.h
Examining data/exonerate-2.4.0/src/struct/sparsecache.h
Examining data/exonerate-2.4.0/src/struct/dejavu.h
Examining data/exonerate-2.4.0/src/struct/bitarray.h
Examining data/exonerate-2.4.0/src/struct/splaytree.h
Examining data/exonerate-2.4.0/src/struct/noitree.h
Examining data/exonerate-2.4.0/src/general/argument.test.c
Examining data/exonerate-2.4.0/src/general/argument.c
Examining data/exonerate-2.4.0/src/general/lineparse.test.c
Examining data/exonerate-2.4.0/src/general/lineparse.c
Examining data/exonerate-2.4.0/src/general/compoundfile.test.c
Examining data/exonerate-2.4.0/src/general/compoundfile.c
Examining data/exonerate-2.4.0/src/general/socket.test.c
Examining data/exonerate-2.4.0/src/general/socket.c
Examining data/exonerate-2.4.0/src/general/jobqueue.test.c
Examining data/exonerate-2.4.0/src/general/jobqueue.c
Examining data/exonerate-2.4.0/src/general/threadref.test.c
Examining data/exonerate-2.4.0/src/general/threadref.c
Examining data/exonerate-2.4.0/src/general/argument.h
Examining data/exonerate-2.4.0/src/general/lineparse.h
Examining data/exonerate-2.4.0/src/general/compoundfile.h
Examining data/exonerate-2.4.0/src/general/socket.h
Examining data/exonerate-2.4.0/src/general/jobqueue.h
Examining data/exonerate-2.4.0/src/general/threadref.h
Examining data/exonerate-2.4.0/src/sequence/sequence.test.c
Examining data/exonerate-2.4.0/src/sequence/sequence.c
Examining data/exonerate-2.4.0/src/sequence/alphabet.c
Examining data/exonerate-2.4.0/src/sequence/translate.c
Examining data/exonerate-2.4.0/src/sequence/splice.c
Examining data/exonerate-2.4.0/src/sequence/submat.test.c
Examining data/exonerate-2.4.0/src/sequence/submat.c
Examining data/exonerate-2.4.0/src/sequence/translate.test.c
Examining data/exonerate-2.4.0/src/sequence/splice.test.c
Examining data/exonerate-2.4.0/src/sequence/alphabet.test.c
Examining data/exonerate-2.4.0/src/sequence/codonsubmat.test.c
Examining data/exonerate-2.4.0/src/sequence/codonsubmat.c
Examining data/exonerate-2.4.0/src/sequence/sequence.h
Examining data/exonerate-2.4.0/src/sequence/submat.h
Examining data/exonerate-2.4.0/src/sequence/translate.h
Examining data/exonerate-2.4.0/src/sequence/splice.h
Examining data/exonerate-2.4.0/src/sequence/alphabet.h
Examining data/exonerate-2.4.0/src/sequence/codonsubmat.h
Examining data/exonerate-2.4.0/src/comparison/wordhood.test.c
Examining data/exonerate-2.4.0/src/comparison/wordhood.c
Examining data/exonerate-2.4.0/src/comparison/hspset.test.c
Examining data/exonerate-2.4.0/src/comparison/hspset.c
Examining data/exonerate-2.4.0/src/comparison/match.c
Examining data/exonerate-2.4.0/src/comparison/pcr.test.c
Examining data/exonerate-2.4.0/src/comparison/pcr.c
Examining data/exonerate-2.4.0/src/comparison/comparison.test.c
Examining data/exonerate-2.4.0/src/comparison/comparison.c
Examining data/exonerate-2.4.0/src/comparison/match.test.c
Examining data/exonerate-2.4.0/src/comparison/seeder.test.c
Examining data/exonerate-2.4.0/src/comparison/seeder.c
Examining data/exonerate-2.4.0/src/comparison/wordhood.h
Examining data/exonerate-2.4.0/src/comparison/hspset.h
Examining data/exonerate-2.4.0/src/comparison/pcr.h
Examining data/exonerate-2.4.0/src/comparison/comparison.h
Examining data/exonerate-2.4.0/src/comparison/match.h
Examining data/exonerate-2.4.0/src/comparison/seeder.h
Examining data/exonerate-2.4.0/src/database/fastadb.test.c
Examining data/exonerate-2.4.0/src/database/fastadb.c
Examining data/exonerate-2.4.0/src/database/fastapipe.test.c
Examining data/exonerate-2.4.0/src/database/fastapipe.c
Examining data/exonerate-2.4.0/src/database/dataset.test.c
Examining data/exonerate-2.4.0/src/database/index.test.c
Examining data/exonerate-2.4.0/src/database/index.c
Examining data/exonerate-2.4.0/src/database/fastadb.h
Examining data/exonerate-2.4.0/src/database/fastapipe.h
Examining data/exonerate-2.4.0/src/database/dataset.h
Examining data/exonerate-2.4.0/src/database/index.h
Examining data/exonerate-2.4.0/src/database/dataset.c
Examining data/exonerate-2.4.0/src/c4/region.test.c
Examining data/exonerate-2.4.0/src/c4/region.c
Examining data/exonerate-2.4.0/src/c4/c4.test.c
Examining data/exonerate-2.4.0/src/c4/c4.c
Examining data/exonerate-2.4.0/src/c4/alignment.test.c
Examining data/exonerate-2.4.0/src/c4/alignment.c
Examining data/exonerate-2.4.0/src/c4/codegen.test.c
Examining data/exonerate-2.4.0/src/c4/codegen.c
Examining data/exonerate-2.4.0/src/c4/optimal.test.c
Examining data/exonerate-2.4.0/src/c4/optimal.c
Examining data/exonerate-2.4.0/src/c4/layout.c
Examining data/exonerate-2.4.0/src/c4/viterbi.c
Examining data/exonerate-2.4.0/src/c4/subopt.c
Examining data/exonerate-2.4.0/src/c4/cgutil.c
Examining data/exonerate-2.4.0/src/c4/layout.test.c
Examining data/exonerate-2.4.0/src/c4/viterbi.test.c
Examining data/exonerate-2.4.0/src/c4/opair.test.c
Examining data/exonerate-2.4.0/src/c4/opair.c
Examining data/exonerate-2.4.0/src/c4/subopt.test.c
Examining data/exonerate-2.4.0/src/c4/cgutil.test.c
Examining data/exonerate-2.4.0/src/c4/region.h
Examining data/exonerate-2.4.0/src/c4/c4.h
Examining data/exonerate-2.4.0/src/c4/alignment.h
Examining data/exonerate-2.4.0/src/c4/codegen.h
Examining data/exonerate-2.4.0/src/c4/optimal.h
Examining data/exonerate-2.4.0/src/c4/layout.h
Examining data/exonerate-2.4.0/src/c4/viterbi.h
Examining data/exonerate-2.4.0/src/c4/opair.h
Examining data/exonerate-2.4.0/src/c4/subopt.h
Examining data/exonerate-2.4.0/src/c4/cgutil.h
Examining data/exonerate-2.4.0/src/bsdp/heuristic.test.c
Examining data/exonerate-2.4.0/src/bsdp/heuristic.c
Examining data/exonerate-2.4.0/src/bsdp/bsdp.test.c
Examining data/exonerate-2.4.0/src/bsdp/bsdp.c
Examining data/exonerate-2.4.0/src/bsdp/hpair.test.c
Examining data/exonerate-2.4.0/src/bsdp/hpair.c
Examining data/exonerate-2.4.0/src/bsdp/sar.c
Examining data/exonerate-2.4.0/src/bsdp/sar.test.c
Examining data/exonerate-2.4.0/src/bsdp/heuristic.h
Examining data/exonerate-2.4.0/src/bsdp/bsdp.h
Examining data/exonerate-2.4.0/src/bsdp/hpair.h
Examining data/exonerate-2.4.0/src/bsdp/sar.h
Examining data/exonerate-2.4.0/src/sdp/sdp.test.c
Examining data/exonerate-2.4.0/src/sdp/sdp.c
Examining data/exonerate-2.4.0/src/sdp/boundary.c
Examining data/exonerate-2.4.0/src/sdp/scheduler.c
Examining data/exonerate-2.4.0/src/sdp/lookahead.c
Examining data/exonerate-2.4.0/src/sdp/straceback.c
Examining data/exonerate-2.4.0/src/sdp/lookahead.test.c
Examining data/exonerate-2.4.0/src/sdp/boundary.test.c
Examining data/exonerate-2.4.0/src/sdp/scheduler.test.c
Examining data/exonerate-2.4.0/src/sdp/straceback.test.c
Examining data/exonerate-2.4.0/src/sdp/scheduler.h
Examining data/exonerate-2.4.0/src/sdp/sdp.h
Examining data/exonerate-2.4.0/src/sdp/lookahead.h
Examining data/exonerate-2.4.0/src/sdp/boundary.h
Examining data/exonerate-2.4.0/src/sdp/straceback.h
Examining data/exonerate-2.4.0/src/model/edit_distance.test.c
Examining data/exonerate-2.4.0/src/model/edit_distance.c
Examining data/exonerate-2.4.0/src/model/affine.test.c
Examining data/exonerate-2.4.0/src/model/affine.c
Examining data/exonerate-2.4.0/src/model/ungapped.c
Examining data/exonerate-2.4.0/src/model/protein2dna.test.c
Examining data/exonerate-2.4.0/src/model/protein2dna.c
Examining data/exonerate-2.4.0/src/model/frameshift.c
Examining data/exonerate-2.4.0/src/model/ner.test.c
Examining data/exonerate-2.4.0/src/model/ner.c
Examining data/exonerate-2.4.0/src/model/est2genome.test.c
Examining data/exonerate-2.4.0/src/model/est2genome.c
Examining data/exonerate-2.4.0/src/model/intron.c
Examining data/exonerate-2.4.0/src/model/ungapped.test.c
Examining data/exonerate-2.4.0/src/model/intron.test.c
Examining data/exonerate-2.4.0/src/model/protein2genome.test.c
Examining data/exonerate-2.4.0/src/model/protein2genome.c
Examining data/exonerate-2.4.0/src/model/phase.c
Examining data/exonerate-2.4.0/src/model/coding2coding.test.c
Examining data/exonerate-2.4.0/src/model/coding2coding.c
Examining data/exonerate-2.4.0/src/model/frameshift.test.c
Examining data/exonerate-2.4.0/src/model/coding2genome.test.c
Examining data/exonerate-2.4.0/src/model/coding2genome.c
Examining data/exonerate-2.4.0/src/model/cdna2genome.test.c
Examining data/exonerate-2.4.0/src/model/cdna2genome.c
Examining data/exonerate-2.4.0/src/model/genome2genome.test.c
Examining data/exonerate-2.4.0/src/model/genome2genome.c
Examining data/exonerate-2.4.0/src/model/phase.test.c
Examining data/exonerate-2.4.0/src/model/modeltype.test.c
Examining data/exonerate-2.4.0/src/model/modeltype.c
Examining data/exonerate-2.4.0/src/model/bootstrapper.c
Examining data/exonerate-2.4.0/src/model/edit_distance.h
Examining data/exonerate-2.4.0/src/model/affine.h
Examining data/exonerate-2.4.0/src/model/protein2dna.h
Examining data/exonerate-2.4.0/src/model/ner.h
Examining data/exonerate-2.4.0/src/model/est2genome.h
Examining data/exonerate-2.4.0/src/model/ungapped.h
Examining data/exonerate-2.4.0/src/model/intron.h
Examining data/exonerate-2.4.0/src/model/protein2genome.h
Examining data/exonerate-2.4.0/src/model/coding2coding.h
Examining data/exonerate-2.4.0/src/model/frameshift.h
Examining data/exonerate-2.4.0/src/model/coding2genome.h
Examining data/exonerate-2.4.0/src/model/genome2genome.h
Examining data/exonerate-2.4.0/src/model/cdna2genome.h
Examining data/exonerate-2.4.0/src/model/phase.h
Examining data/exonerate-2.4.0/src/model/modeltype.h
Examining data/exonerate-2.4.0/src/hub/gam.test.c
Examining data/exonerate-2.4.0/src/hub/gam.c
Examining data/exonerate-2.4.0/src/hub/analysis.test.c
Examining data/exonerate-2.4.0/src/hub/analysis.c
Examining data/exonerate-2.4.0/src/hub/bsam.c
Examining data/exonerate-2.4.0/src/hub/bsam.test.c
Examining data/exonerate-2.4.0/src/hub/gam.h
Examining data/exonerate-2.4.0/src/hub/analysis.h
Examining data/exonerate-2.4.0/src/hub/bsam.h
Examining data/exonerate-2.4.0/src/program/exonerate.c
Examining data/exonerate-2.4.0/src/program/ipcress.c
Examining data/exonerate-2.4.0/src/program/exonerate-server.c
Examining data/exonerate-2.4.0/src/util/fastaclean.c
Examining data/exonerate-2.4.0/src/util/fastaclip.c
Examining data/exonerate-2.4.0/src/util/fastachecksum.c
Examining data/exonerate-2.4.0/src/util/fastacomposition.c
Examining data/exonerate-2.4.0/src/util/fastadiff.c
Examining data/exonerate-2.4.0/src/util/fastaexplode.c
Examining data/exonerate-2.4.0/src/util/fastafetch.c
Examining data/exonerate-2.4.0/src/util/fastahardmask.c
Examining data/exonerate-2.4.0/src/util/fastaindex.c
Examining data/exonerate-2.4.0/src/util/fastalength.c
Examining data/exonerate-2.4.0/src/util/fastanrdb.c
Examining data/exonerate-2.4.0/src/util/fastaoverlap.c
Examining data/exonerate-2.4.0/src/util/fastareformat.c
Examining data/exonerate-2.4.0/src/util/fastaremove.c
Examining data/exonerate-2.4.0/src/util/fastarevcomp.c
Examining data/exonerate-2.4.0/src/util/fastasoftmask.c
Examining data/exonerate-2.4.0/src/util/fastasort.c
Examining data/exonerate-2.4.0/src/util/fastasplit.c
Examining data/exonerate-2.4.0/src/util/fastasubseq.c
Examining data/exonerate-2.4.0/src/util/fastatranslate.c
Examining data/exonerate-2.4.0/src/util/fastavalidcds.c
Examining data/exonerate-2.4.0/src/util/fasta2esd.c
Examining data/exonerate-2.4.0/src/util/fastaannotatecdna.c
Examining data/exonerate-2.4.0/src/util/esd2esi.c
FINAL RESULTS:
data/exonerate-2.4.0/src/c4/codegen.c:227:8: [4] (shell) system:
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(system(compile_command))
data/exonerate-2.4.0/src/model/bootstrapper.c:139:15: [4] (shell) system:
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.
ret_val = system(command);
data/exonerate-2.4.0/src/model/bootstrapper.c:153:15: [4] (shell) system:
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.
ret_val = system(command);
data/exonerate-2.4.0/src/model/bootstrapper.c:186:8: [4] (shell) system:
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(system(command))
data/exonerate-2.4.0/src/hub/gam.c:371:27: [3] (buffer) g_get_tmp_dir:
This function is synonymous with 'getenv("TMP")';it returns untrustable
input if the environment can beset by an attacker. It 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.
g_get_tmp_dir(),
data/exonerate-2.4.0/src/struct/rangetree.c:121:5: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(list->len);
data/exonerate-2.4.0/src/struct/rangetree.c:124:20: [3] (random) lrand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
j = ((gint)lrand48()) % list->len;
data/exonerate-2.4.0/src/c4/codegen.c:119:13: [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).
c->fp = fopen(c->code_path, "w");
data/exonerate-2.4.0/src/database/dataset.c:344:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/database/dataset.c:488:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/database/dataset.c:491:10: [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(path, "w");
data/exonerate-2.4.0/src/database/dataset.c:502:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/database/fastadb.c:255:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/database/index.c:420:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/database/index.c:757:17: [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).
index->fp = fopen(index_path, "r");
data/exonerate-2.4.0/src/database/index.c:763:17: [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).
index->fp = fopen(index_path, "w");
data/exonerate-2.4.0/src/database/index.c:795:17: [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).
index->fp = fopen(index_path, "r");
data/exonerate-2.4.0/src/database/index.c:937:17: [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).
index->fp = fopen(index_path, "r");
data/exonerate-2.4.0/src/general/argument.c:657:18: [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).
(*dst_int) = atoi(arg_string);
data/exonerate-2.4.0/src/general/compoundfile.c:44:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/general/lineparse.test.c:25:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/general/socket.c:76:5: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
bcopy(hp->h_addr, &server.sin_addr, hp->h_length);
data/exonerate-2.4.0/src/general/socket.c:125:31: [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).
line_expect = atoi(&buffer[11]);
data/exonerate-2.4.0/src/general/socket.test.c:83:12: [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).
port = atoi(argv[3]);
data/exonerate-2.4.0/src/hub/analysis.c:405:16: [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).
port = atoi(path+divider+1);
data/exonerate-2.4.0/src/hub/analysis.c:671:11: [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).
len = atoi(word[0]);
data/exonerate-2.4.0/src/hub/analysis.c:672:16: [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).
checksum = atoi(word[1]);
data/exonerate-2.4.0/src/hub/analysis.c:795:11: [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).
len = atoi(seqinfo_word[0]);
data/exonerate-2.4.0/src/hub/analysis.c:796:16: [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).
checksum = atoi(seqinfo_word[1]);
data/exonerate-2.4.0/src/hub/analysis.c:1137:18: [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(path, "r");
data/exonerate-2.4.0/src/hub/gam.c:376:10: [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(path, "w+");
data/exonerate-2.4.0/src/model/bootstrapper.c:78:21: [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).
bs->header_fp = fopen(bs->header_path, "w");
data/exonerate-2.4.0/src/model/bootstrapper.c:81:21: [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).
bs->lookup_fp = fopen(bs->lookup_path, "w");
data/exonerate-2.4.0/src/program/exonerate-server.c:433:33: [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).
register gint seed_repeat = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:446:37: [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).
register gint dnahspthreshold = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:457:41: [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).
register gint proteinhspthreshold = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:469:39: [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).
register gint codonhspthreshold = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:483:34: [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).
register gint dnawordlimit = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:494:38: [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).
register gint proteinwordlimit = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:506:36: [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).
register gint codonwordlimit = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:520:35: [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).
register gint dnahspdropoff = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:531:39: [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).
register gint proteinhspdropoff = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:543:37: [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).
register gint codonhspdropoff = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:557:40: [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).
register gint geneseed_threshold = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:566:37: [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).
register gint geneseed_repeat = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:575:35: [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).
register gint max_query_span= atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:584:36: [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).
register gint max_target_span= atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:695:31: [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).
num = atoi(word_list->pdata[2]);
data/exonerate-2.4.0/src/program/exonerate-server.c:703:31: [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).
num = atoi(word_list->pdata[2]);
data/exonerate-2.4.0/src/program/exonerate-server.c:711:31: [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).
num = atoi(word_list->pdata[2]);
data/exonerate-2.4.0/src/program/exonerate-server.c:712:33: [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).
start = atoi(word_list->pdata[3]);
data/exonerate-2.4.0/src/program/exonerate-server.c:713:31: [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).
len = atoi(word_list->pdata[4]);
data/exonerate-2.4.0/src/program/ipcress.c:234:25: [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).
ipcress->input_fp = fopen(ipcress_path, "r");
data/exonerate-2.4.0/src/program/ipcress.c:266:27: [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).
min_product_len = atoi(ipcress->input_lp->word->pdata[3]);
data/exonerate-2.4.0/src/program/ipcress.c:267:27: [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).
max_product_len = atoi(ipcress->input_lp->word->pdata[4]);
data/exonerate-2.4.0/src/sequence/sequence.c:52:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/sequence/sequence.c:74:29: [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).
cds_start = atoi(lp->word->pdata[2]) - 1;
data/exonerate-2.4.0/src/sequence/sequence.c:75:30: [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).
cds_length = atoi(lp->word->pdata[3]);
data/exonerate-2.4.0/src/sequence/splice.c:123:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/sequence/submat.c:224:25: [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).
register FILE *fp = fopen(path, "r");
data/exonerate-2.4.0/src/sequence/translate.c:213:14: [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).
id = atoi(code);
data/exonerate-2.4.0/src/struct/fsm.c:38:5: [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(f->insertion_filter, f->index, sizeof(gchar)*ALPHABETSIZE);
data/exonerate-2.4.0/src/struct/fsm.c:39:5: [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(f->traversal_filter, f->index, sizeof(gchar)*ALPHABETSIZE);
data/exonerate-2.4.0/src/struct/fsm.c:206:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, f->index, sizeof(gchar)*ALPHABETSIZE);
data/exonerate-2.4.0/src/struct/fsm.test.c:42:5: [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 *testset[TESTSETSIZE] = { /* C KEYWORDS */
data/exonerate-2.4.0/src/util/fasta2esd.c:47:10: [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(output_path, "r");
data/exonerate-2.4.0/src/util/fastaexplode.c:26:25: [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).
register FILE *fp = fopen(output_path, "r");
data/exonerate-2.4.0/src/util/fastaexplode.c:31:10: [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(output_path, "w");
data/exonerate-2.4.0/src/util/fastafetch.c:125:19: [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).
fp = fopen(query, "r");
data/exonerate-2.4.0/src/util/fastafetch.c:145:31: [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).
register FILE *index_fp = fopen(index_path, "r");
data/exonerate-2.4.0/src/util/fastaindex.c:38:10: [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(index_path, "r");
data/exonerate-2.4.0/src/util/fastaindex.c:43:10: [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(index_path, "w");
data/exonerate-2.4.0/src/util/fastaremove.c:76:21: [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).
remove_fp = fopen(remove_path, "r");
data/exonerate-2.4.0/src/util/fastasplit.c:29:10: [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(path, "w");
data/exonerate-2.4.0/src/c4/alignment.c:243:28: [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).
register gint maxlen = strlen(tmpstr);
data/exonerate-2.4.0/src/c4/alignment.c:380:14: [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).
g_assert(strlen(query_string) == strlen(match_string));
data/exonerate-2.4.0/src/c4/alignment.c:380:38: [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).
g_assert(strlen(query_string) == strlen(match_string));
data/exonerate-2.4.0/src/c4/alignment.c:381:14: [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).
g_assert(strlen(match_string) == strlen(target_string));
data/exonerate-2.4.0/src/c4/alignment.c:381:38: [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).
g_assert(strlen(match_string) == strlen(target_string));
data/exonerate-2.4.0/src/c4/alignment.c:384:22: [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).
g_assert(strlen(match_string)
data/exonerate-2.4.0/src/c4/alignment.c:385:22: [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(inner_query_string));
data/exonerate-2.4.0/src/c4/alignment.c:388:21: [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).
for(i = strlen(match_string)-1; i >=0; i--)
data/exonerate-2.4.0/src/c4/alignment.c:394:22: [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).
g_assert(strlen(match_string)
data/exonerate-2.4.0/src/c4/alignment.c:395:22: [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(inner_target_string));
data/exonerate-2.4.0/src/c4/alignment.c:398:21: [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).
for(i = strlen(match_string)-1; i >=0; i--)
data/exonerate-2.4.0/src/c4/alignment.c:572:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq_string, Alphabet_aa2tla(seq_string[0]), 3);
data/exonerate-2.4.0/src/c4/alignment.c:737:14: [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).
g_assert(strlen(name_string) > strlen(label));
data/exonerate-2.4.0/src/c4/alignment.c:737:36: [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).
g_assert(strlen(name_string) > strlen(label));
data/exonerate-2.4.0/src/c4/alignment.c:738:13: [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).
fill = (strlen(name_string)-strlen(label))+1;
data/exonerate-2.4.0/src/c4/alignment.c:738:33: [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).
fill = (strlen(name_string)-strlen(label))+1;
data/exonerate-2.4.0/src/c4/alignment.c:741:29: [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).
gap_string = g_strnfill(strlen(name_string), '.');
data/exonerate-2.4.0/src/c4/alignment.c:742:29: [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).
pad_string = g_strnfill(strlen(name_string), '^');
data/exonerate-2.4.0/src/c4/alignment.c:743:14: [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).
g_assert(strlen(name_string) == strlen(middle_string));
data/exonerate-2.4.0/src/c4/alignment.c:743:37: [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).
g_assert(strlen(name_string) == strlen(middle_string));
data/exonerate-2.4.0/src/c4/alignment.c:744:14: [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).
g_assert(strlen(middle_string) == strlen(gap_string));
data/exonerate-2.4.0/src/c4/alignment.c:744:39: [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).
g_assert(strlen(middle_string) == strlen(gap_string));
data/exonerate-2.4.0/src/c4/alignment.c:780:31: [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).
register gint upper_len = strlen(upper_string),
data/exonerate-2.4.0/src/c4/alignment.c:781:32: [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).
middle_len = strlen(middle_string),
data/exonerate-2.4.0/src/c4/alignment.c:782:31: [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).
lower_len = strlen(lower_string),
data/exonerate-2.4.0/src/c4/alignment.c:1066:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq_string, Alphabet_aa2tla(seq_string[0]), 3);
data/exonerate-2.4.0/src/c4/c4.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).
register GString *s = g_string_sized_new(strlen(str)+10);
data/exonerate-2.4.0/src/c4/codegen.c:42:58: [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).
register GString *file_name_str = g_string_sized_new(strlen(name));
data/exonerate-2.4.0/src/c4/codegen.c:141:48: [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).
register GString *str = g_string_sized_new(strlen(format));
data/exonerate-2.4.0/src/c4/viterbi.c:873:48: [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).
register GString *str = g_string_sized_new(strlen(macro));
data/exonerate-2.4.0/src/comparison/hspset.c:606:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant string.
strncpy(equiv_str, "###", hd->max_advance);
data/exonerate-2.4.0/src/comparison/hspset.c:619:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant string.
strncpy(query_str, "###", hd->max_advance);
data/exonerate-2.4.0/src/comparison/hspset.c:632:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant string.
strncpy(target_str, "###", hd->max_advance);
data/exonerate-2.4.0/src/comparison/pcr.c:37:41: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
gint mismatch){
data/exonerate-2.4.0/src/comparison/pcr.c:42:27: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
pcr_match->mismatch = mismatch;
data/exonerate-2.4.0/src/comparison/pcr.c:57:51: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
Sequence_Strand strand, gchar *probe, gint mismatch){
data/exonerate-2.4.0/src/comparison/pcr.c:63:27: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
pcr_probe->mismatch = mismatch;
data/exonerate-2.4.0/src/comparison/pcr.c:80:60: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
register gint i, product_length, mismatch = pcr_probe->mismatch;
data/exonerate-2.4.0/src/comparison/pcr.c:99:20: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(mismatch > pcr->mismatch_threshold)
data/exonerate-2.4.0/src/comparison/pcr.c:109:20: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(mismatch > pcr->mismatch_threshold)
data/exonerate-2.4.0/src/comparison/pcr.c:126:58: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
pcr_match = PCR_Match_create(pcr_probe, match_start, mismatch);
data/exonerate-2.4.0/src/comparison/pcr.c:210:53: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
Sequence_Strand strand, gchar *primer, gint mismatch){
data/exonerate-2.4.0/src/comparison/pcr.c:212:31: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
strand, primer, mismatch);
data/exonerate-2.4.0/src/comparison/pcr.c:227:15: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
word, mismatch);
data/exonerate-2.4.0/src/comparison/pcr.c:230:15: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
word, mismatch);
data/exonerate-2.4.0/src/comparison/pcr.c:241:26: [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).
pcr_primer->length = strlen(primer);
data/exonerate-2.4.0/src/comparison/pcr.c:331:29: [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).
+ (sizeof(gchar) * strlen(pcr_experiment->id))
data/exonerate-2.4.0/src/comparison/pcr.h:43:24: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
gint mismatch;
data/exonerate-2.4.0/src/comparison/pcr.h:50:16: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
gint mismatch;
data/exonerate-2.4.0/src/comparison/seeder.c:287:17: [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((gchar*)comparison_alphabet->member);
data/exonerate-2.4.0/src/comparison/seeder.c:737:14: [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).
|| ((strlen(ambig) * curr_state_list_len)
data/exonerate-2.4.0/src/comparison/seeder.c:807:14: [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).
|| ((strlen(ambig) * curr_state_list_len)
data/exonerate-2.4.0/src/comparison/wordhood.c:253:12: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
return strncpy(wh->curr_word+wh->word_pos,
data/exonerate-2.4.0/src/comparison/wordhood.test.c:41:52: [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).
WordHood_traverse(wh, wordhood_test_func, seq, strlen(seq), &count);
data/exonerate-2.4.0/src/comparison/wordhood.test.c:51:52: [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).
WordHood_traverse(wh, wordhood_test_func, seq, strlen(seq), &count);
data/exonerate-2.4.0/src/database/dataset.c:164:27: [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).
+ (sizeof(gchar)*strlen(ds->id))
data/exonerate-2.4.0/src/database/dataset.c:165:36: [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).
+ (sizeof(gchar)*(ds->def?strlen(ds->id):0))
data/exonerate-2.4.0/src/database/dataset.c:256:28: [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).
path_data_size += (strlen(path) + 1);
data/exonerate-2.4.0/src/database/dataset.c:262:27: [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).
seq_data_size += (strlen(ds->id) + 1);
data/exonerate-2.4.0/src/database/dataset.c:264:31: [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).
seq_data_size += (strlen(ds->def) + 1);
data/exonerate-2.4.0/src/database/dataset.c:371:31: [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).
path = g_strndup(buf, strlen(buf)-1);
data/exonerate-2.4.0/src/database/dataset.c:474:26: [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).
seq_offset = 1 + strlen(ds->id)
data/exonerate-2.4.0/src/database/dataset.c:475:31: [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).
+ (ds->def?strlen(ds->def)+1:0);
data/exonerate-2.4.0/src/database/fastadb.c:87:21: [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).
for(i = strlen(path)-1; i >= 0; i--)
data/exonerate-2.4.0/src/database/fastadb.c:260:18: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(((ch = getc(fp)) != EOF)){
data/exonerate-2.4.0/src/database/fastadb.c:491:32: [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).
register gint seq_offset = strlen(fdbs->seq->id) + 2
data/exonerate-2.4.0/src/database/fastadb.c:492:51: [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).
+ (fdbs->seq->def ? (strlen(fdbs->seq->def)+1) : 0);
data/exonerate-2.4.0/src/database/index.c:247:14: [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).
|| ((strlen(ambig) * curr_state_list_len)
data/exonerate-2.4.0/src/database/index.c:768:41: [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).
index->header = Index_Header_create(strlen(dataset_path),
data/exonerate-2.4.0/src/general/argument.c:174:8: [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).
if(strlen(branch) >= 10)
data/exonerate-2.4.0/src/general/argument.c:175:42: [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).
g_print("Branch: %.*s\n", (gint)(strlen(branch)-9), branch+7);
data/exonerate-2.4.0/src/general/argument.c:344:21: [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).
for(j = strlen(as->desc); j > 0; j--)
data/exonerate-2.4.0/src/general/argument.c:378:21: [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).
for(j = strlen(as->desc); j > 0; j--)
data/exonerate-2.4.0/src/general/argument.c:417:13: [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).
for(i = strlen(ao->env_var)-1; i >= 0; i--)
data/exonerate-2.4.0/src/general/compoundfile.c:219:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cf->in_buffer_full = read(fileno(cf->fp), cf->in_buffer, read_size);
data/exonerate-2.4.0/src/general/jobqueue.c:50:13: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(1000); /* wait before checking job queue again */
data/exonerate-2.4.0/src/general/jobqueue.c:123:9: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(1000); /* wait before checking if queue is empty again */
data/exonerate-2.4.0/src/general/jobqueue.test.c:22:5: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(1000000); /* test job length */
data/exonerate-2.4.0/src/general/lineparse.c:37:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(lp->fp)) != EOF){ /* read a line */
data/exonerate-2.4.0/src/general/lineparse.c:75:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(lp->fp)) != EOF){
data/exonerate-2.4.0/src/general/socket.c:150:44: [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).
register gint start = 0, len, msglen = strlen(msg);
data/exonerate-2.4.0/src/general/socket.c:163:53: [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).
register GString *full_msg = g_string_sized_new(strlen(msg)+32);
data/exonerate-2.4.0/src/hub/analysis.c:428:42: [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).
if((aclient->verbosity == 3) && (strlen(reply) >= 80))
data/exonerate-2.4.0/src/hub/analysis.c:451:39: [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, expect, strlen(expect))){
data/exonerate-2.4.0/src/hub/analysis.c:750:16: [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).
page_len = strlen(reply+8)-1;
data/exonerate-2.4.0/src/hub/analysis.c:800:11: [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).
if(id[strlen(id)-1] == '\n')
data/exonerate-2.4.0/src/hub/analysis.c:801:12: [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).
id[strlen(id)-1] = '\0';
data/exonerate-2.4.0/src/hub/analysis.c:802:20: [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).
if(def && (def[strlen(def)-1] == '\n'))
data/exonerate-2.4.0/src/hub/analysis.c:803:13: [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).
def[strlen(def)-1] = '\0';
data/exonerate-2.4.0/src/hub/gam.c:197:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ch = getc(gam->bestn_tmp_file);
data/exonerate-2.4.0/src/model/edit_distance.c:25:22: [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).
edd->query_len = strlen(query);
data/exonerate-2.4.0/src/model/edit_distance.c:26:23: [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).
edd->target_len = strlen(target);
data/exonerate-2.4.0/src/program/exonerate-server.c:645:29: [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).
register gint msg_len = strlen(msg);
data/exonerate-2.4.0/src/program/exonerate-server.c:807:41: [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).
if((server->verbosity == 3) && (strlen(*reply) >= 80))
data/exonerate-2.4.0/src/program/ipcress.c:138:43: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
primer_a->length-match_a->mismatch,
data/exonerate-2.4.0/src/program/ipcress.c:140:43: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
primer_b->length-match_b->mismatch,
data/exonerate-2.4.0/src/program/ipcress.c:201:18: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
match_a->mismatch,
data/exonerate-2.4.0/src/program/ipcress.c:205:18: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
match_b->mismatch,
data/exonerate-2.4.0/src/sequence/sequence.c:208:30: [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).
s->len = len ? len : strlen(seq);
data/exonerate-2.4.0/src/sequence/sequence.c:209:39: [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).
g_assert((!len) || (s->len == strlen(seq)));
data/exonerate-2.4.0/src/sequence/sequence.c:802:26: [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).
+ sizeof(gchar)*strlen(s->id)
data/exonerate-2.4.0/src/sequence/sequence.c:803:34: [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).
+ sizeof(gchar)*(s->def?strlen(s->def):0)
data/exonerate-2.4.0/src/sequence/splice.c:195:21: [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).
if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate")))
data/exonerate-2.4.0/src/sequence/splice.c:203:21: [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).
if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate")))
data/exonerate-2.4.0/src/sequence/splice.test.c:22:25: [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).
register gint len = strlen(seq);
data/exonerate-2.4.0/src/sequence/submat.c:230:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){
data/exonerate-2.4.0/src/sequence/submat.c:248:19: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} while((ch = getc(fp)) != EOF);
data/exonerate-2.4.0/src/sequence/submat.c:251:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){ /* Read data */
data/exonerate-2.4.0/src/sequence/translate.c:133:23: [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).
g_assert(code && (strlen(code) == 64));
data/exonerate-2.4.0/src/sequence/translate.c:209:11: [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).
len = strlen(code);
data/exonerate-2.4.0/src/struct/dejavu.test.c:36:46: [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).
register DejaVu *dv = DejaVu_create(seq, strlen(seq));
data/exonerate-2.4.0/src/struct/fsm.test.c:60:32: [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).
FSM_add(f, testset[i], strlen(testset[i]), GINT_TO_POINTER(1));
data/exonerate-2.4.0/src/struct/vfsm.c:37:27: [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).
vfsm->alphabet_size = strlen(alphabet);
data/exonerate-2.4.0/src/util/fastafetch.c:26:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){
data/exonerate-2.4.0/src/util/fastafetch.c:36:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){
data/exonerate-2.4.0/src/util/fastafetch.c:107:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){
data/exonerate-2.4.0/src/util/fastaremove.c:37:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((ch = getc(fp)) != EOF){
ANALYSIS SUMMARY:
Hits = 191
Lines analyzed = 52889 in approximately 1.35 seconds (39259 lines/second)
Physical Source Lines of Code (SLOC) = 42418
Hits@level = [0] 112 [1] 117 [2] 67 [3] 3 [4] 4 [5] 0
Hits@level+ = [0+] 303 [1+] 191 [2+] 74 [3+] 7 [4+] 4 [5+] 0
Hits/KSLOC@level+ = [0+] 7.14319 [1+] 4.50281 [2+] 1.74454 [3+] 0.165024 [4+] 0.0942996 [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.