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/vt-0.57721+ds/ahmm.cpp
Examining data/vt-0.57721+ds/ahmm.h
Examining data/vt-0.57721+ds/align.cpp
Examining data/vt-0.57721+ds/align.h
Examining data/vt-0.57721+ds/allele.cpp
Examining data/vt-0.57721+ds/allele.h
Examining data/vt-0.57721+ds/annotate_1000g.cpp
Examining data/vt-0.57721+ds/annotate_1000g.h
Examining data/vt-0.57721+ds/annotate_dbsnp_rsid.cpp
Examining data/vt-0.57721+ds/annotate_dbsnp_rsid.h
Examining data/vt-0.57721+ds/annotate_indels.cpp
Examining data/vt-0.57721+ds/annotate_indels.h
Examining data/vt-0.57721+ds/annotate_indels2.cpp
Examining data/vt-0.57721+ds/annotate_indels2.h
Examining data/vt-0.57721+ds/annotate_regions.cpp
Examining data/vt-0.57721+ds/annotate_regions.h
Examining data/vt-0.57721+ds/annotate_variants.cpp
Examining data/vt-0.57721+ds/annotate_variants.h
Examining data/vt-0.57721+ds/annotate_vntrs.cpp
Examining data/vt-0.57721+ds/annotate_vntrs.h
Examining data/vt-0.57721+ds/augmented_bam_record.cpp
Examining data/vt-0.57721+ds/augmented_bam_record.h
Examining data/vt-0.57721+ds/bam_ordered_reader.cpp
Examining data/vt-0.57721+ds/bam_ordered_reader.h
Examining data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp
Examining data/vt-0.57721+ds/bcf_genotyping_buffered_reader.h
Examining data/vt-0.57721+ds/bcf_ordered_reader.cpp
Examining data/vt-0.57721+ds/bcf_ordered_reader.h
Examining data/vt-0.57721+ds/bcf_ordered_writer.h
Examining data/vt-0.57721+ds/bcf_single_genotyping_buffered_reader.cpp
Examining data/vt-0.57721+ds/bcf_single_genotyping_buffered_reader.h
Examining data/vt-0.57721+ds/bcf_synced_reader.cpp
Examining data/vt-0.57721+ds/bcf_synced_reader.h
Examining data/vt-0.57721+ds/bed.cpp
Examining data/vt-0.57721+ds/bed.h
Examining data/vt-0.57721+ds/candidate_motif_picker.cpp
Examining data/vt-0.57721+ds/candidate_motif_picker.h
Examining data/vt-0.57721+ds/candidate_region_extractor.cpp
Examining data/vt-0.57721+ds/candidate_region_extractor.h
Examining data/vt-0.57721+ds/cat.cpp
Examining data/vt-0.57721+ds/cat.h
Examining data/vt-0.57721+ds/chmm.cpp
Examining data/vt-0.57721+ds/chmm.h
Examining data/vt-0.57721+ds/circular_buffer.h
Examining data/vt-0.57721+ds/complex_genotyping_record.cpp
Examining data/vt-0.57721+ds/complex_genotyping_record.h
Examining data/vt-0.57721+ds/compute_concordance.cpp
Examining data/vt-0.57721+ds/compute_concordance.h
Examining data/vt-0.57721+ds/compute_features.cpp
Examining data/vt-0.57721+ds/compute_features.h
Examining data/vt-0.57721+ds/compute_features2.cpp
Examining data/vt-0.57721+ds/compute_features2.h
Examining data/vt-0.57721+ds/compute_rl_dist.cpp
Examining data/vt-0.57721+ds/compute_rl_dist.h
Examining data/vt-0.57721+ds/config.cpp
Examining data/vt-0.57721+ds/config.h
Examining data/vt-0.57721+ds/consolidate.cpp
Examining data/vt-0.57721+ds/consolidate_adjacent_vntrs.cpp
Examining data/vt-0.57721+ds/consolidate_adjacent_vntrs.h
Examining data/vt-0.57721+ds/consolidate_multiallelics.cpp
Examining data/vt-0.57721+ds/consolidate_multiallelics.h
Examining data/vt-0.57721+ds/consolidate_vntrs.cpp
Examining data/vt-0.57721+ds/consolidate_vntrs.h
Examining data/vt-0.57721+ds/construct_probes.cpp
Examining data/vt-0.57721+ds/construct_probes.h
Examining data/vt-0.57721+ds/decompose.cpp
Examining data/vt-0.57721+ds/decompose.h
Examining data/vt-0.57721+ds/decompose2.cpp
Examining data/vt-0.57721+ds/decompose2.h
Examining data/vt-0.57721+ds/decompose_blocksub.cpp
Examining data/vt-0.57721+ds/decompose_blocksub.h
Examining data/vt-0.57721+ds/discover.cpp
Examining data/vt-0.57721+ds/duplicate.cpp
Examining data/vt-0.57721+ds/duplicate.h
Examining data/vt-0.57721+ds/estimate.cpp
Examining data/vt-0.57721+ds/estimate.h
Examining data/vt-0.57721+ds/estimator.cpp
Examining data/vt-0.57721+ds/extract_vntrs.cpp
Examining data/vt-0.57721+ds/extract_vntrs.h
Examining data/vt-0.57721+ds/filter.cpp
Examining data/vt-0.57721+ds/filter.h
Examining data/vt-0.57721+ds/filter_overlap.cpp
Examining data/vt-0.57721+ds/filter_overlap.h
Examining data/vt-0.57721+ds/flank_detector.cpp
Examining data/vt-0.57721+ds/flank_detector.h
Examining data/vt-0.57721+ds/fuzzy_aligner.cpp
Examining data/vt-0.57721+ds/fuzzy_aligner.h
Examining data/vt-0.57721+ds/fuzzy_partition.cpp
Examining data/vt-0.57721+ds/fuzzy_partition.h
Examining data/vt-0.57721+ds/gencode.cpp
Examining data/vt-0.57721+ds/gencode.h
Examining data/vt-0.57721+ds/genome_interval.cpp
Examining data/vt-0.57721+ds/genome_interval.h
Examining data/vt-0.57721+ds/genotype.cpp
Examining data/vt-0.57721+ds/genotype.h
Examining data/vt-0.57721+ds/genotyping_record.cpp
Examining data/vt-0.57721+ds/genotyping_record.h
Examining data/vt-0.57721+ds/ghmm.cpp
Examining data/vt-0.57721+ds/ghmm.h
Examining data/vt-0.57721+ds/hfilter.cpp
Examining data/vt-0.57721+ds/hfilter.h
Examining data/vt-0.57721+ds/indel_annotator.cpp
Examining data/vt-0.57721+ds/indel_annotator.h
Examining data/vt-0.57721+ds/indel_genotyping_record.cpp
Examining data/vt-0.57721+ds/indel_genotyping_record.h
Examining data/vt-0.57721+ds/index.cpp
Examining data/vt-0.57721+ds/index.h
Examining data/vt-0.57721+ds/info2tab.cpp
Examining data/vt-0.57721+ds/info2tab.h
Examining data/vt-0.57721+ds/interval.cpp
Examining data/vt-0.57721+ds/interval.h
Examining data/vt-0.57721+ds/interval_tree.cpp
Examining data/vt-0.57721+ds/interval_tree.h
Examining data/vt-0.57721+ds/large_motif_tree.cpp
Examining data/vt-0.57721+ds/large_motif_tree.h
Examining data/vt-0.57721+ds/lfhmm.cpp
Examining data/vt-0.57721+ds/lfhmm.h
Examining data/vt-0.57721+ds/lhmm.cpp
Examining data/vt-0.57721+ds/lhmm.h
Examining data/vt-0.57721+ds/lhmm1.cpp
Examining data/vt-0.57721+ds/lhmm1.h
Examining data/vt-0.57721+ds/liftover.cpp
Examining data/vt-0.57721+ds/liftover.h
Examining data/vt-0.57721+ds/log_tool.cpp
Examining data/vt-0.57721+ds/log_tool.h
Examining data/vt-0.57721+ds/main.cpp
Examining data/vt-0.57721+ds/merge.cpp
Examining data/vt-0.57721+ds/merge.h
Examining data/vt-0.57721+ds/merge_candidate_variants.cpp
Examining data/vt-0.57721+ds/merge_candidate_variants.h
Examining data/vt-0.57721+ds/merge_genotypes.cpp
Examining data/vt-0.57721+ds/merge_genotypes.h
Examining data/vt-0.57721+ds/milk_filter.h
Examining data/vt-0.57721+ds/motif_map.cpp
Examining data/vt-0.57721+ds/motif_map.h
Examining data/vt-0.57721+ds/motif_tree.cpp
Examining data/vt-0.57721+ds/motif_tree.h
Examining data/vt-0.57721+ds/multi_partition.cpp
Examining data/vt-0.57721+ds/multi_partition.h
Examining data/vt-0.57721+ds/multiallelics_consolidator.cpp
Examining data/vt-0.57721+ds/needle.cpp
Examining data/vt-0.57721+ds/needle.h
Examining data/vt-0.57721+ds/normalize.h
Examining data/vt-0.57721+ds/nuclear_pedigree.cpp
Examining data/vt-0.57721+ds/nuclear_pedigree.h
Examining data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp
Examining data/vt-0.57721+ds/ordered_bcf_overlap_matcher.h
Examining data/vt-0.57721+ds/ordered_region_overlap_matcher.cpp
Examining data/vt-0.57721+ds/ordered_region_overlap_matcher.h
Examining data/vt-0.57721+ds/partition.cpp
Examining data/vt-0.57721+ds/partition.h
Examining data/vt-0.57721+ds/paste.cpp
Examining data/vt-0.57721+ds/paste.h
Examining data/vt-0.57721+ds/paste_and_compute_features_sequential.cpp
Examining data/vt-0.57721+ds/paste_and_compute_features_sequential.h
Examining data/vt-0.57721+ds/paste_genotypes.h
Examining data/vt-0.57721+ds/pedigree.cpp
Examining data/vt-0.57721+ds/pedigree.h
Examining data/vt-0.57721+ds/peek.cpp
Examining data/vt-0.57721+ds/peek.h
Examining data/vt-0.57721+ds/pileup.h
Examining data/vt-0.57721+ds/pregex.cpp
Examining data/vt-0.57721+ds/pregex.h
Examining data/vt-0.57721+ds/profile_afs.cpp
Examining data/vt-0.57721+ds/profile_afs.h
Examining data/vt-0.57721+ds/profile_chm1.cpp
Examining data/vt-0.57721+ds/profile_chm1.h
Examining data/vt-0.57721+ds/profile_chrom.cpp
Examining data/vt-0.57721+ds/profile_chrom.h
Examining data/vt-0.57721+ds/profile_fic_hwe.cpp
Examining data/vt-0.57721+ds/profile_fic_hwe.h
Examining data/vt-0.57721+ds/profile_hwe.cpp
Examining data/vt-0.57721+ds/profile_hwe.h
Examining data/vt-0.57721+ds/profile_indels.cpp
Examining data/vt-0.57721+ds/profile_indels.h
Examining data/vt-0.57721+ds/profile_len.cpp
Examining data/vt-0.57721+ds/profile_len.h
Examining data/vt-0.57721+ds/profile_mendelian.cpp
Examining data/vt-0.57721+ds/profile_mendelian.h
Examining data/vt-0.57721+ds/profile_na12878.cpp
Examining data/vt-0.57721+ds/profile_na12878.h
Examining data/vt-0.57721+ds/profile_snps.cpp
Examining data/vt-0.57721+ds/profile_snps.h
Examining data/vt-0.57721+ds/profile_vntrs.cpp
Examining data/vt-0.57721+ds/profile_vntrs.h
Examining data/vt-0.57721+ds/program.cpp
Examining data/vt-0.57721+ds/program.h
Examining data/vt-0.57721+ds/read_filter.cpp
Examining data/vt-0.57721+ds/read_filter.h
Examining data/vt-0.57721+ds/reference_sequence.h
Examining data/vt-0.57721+ds/rfhmm.cpp
Examining data/vt-0.57721+ds/rfhmm.h
Examining data/vt-0.57721+ds/rfhmm_x.cpp
Examining data/vt-0.57721+ds/rfhmm_x.h
Examining data/vt-0.57721+ds/rminfo.cpp
Examining data/vt-0.57721+ds/rminfo.h
Examining data/vt-0.57721+ds/seq.cpp
Examining data/vt-0.57721+ds/seq.h
Examining data/vt-0.57721+ds/set_ref.cpp
Examining data/vt-0.57721+ds/set_ref.h
Examining data/vt-0.57721+ds/snp_genotyping_record.cpp
Examining data/vt-0.57721+ds/snp_genotyping_record.h
Examining data/vt-0.57721+ds/sort.cpp
Examining data/vt-0.57721+ds/sort.h
Examining data/vt-0.57721+ds/subset.cpp
Examining data/vt-0.57721+ds/subset.h
Examining data/vt-0.57721+ds/sv_tree.cpp
Examining data/vt-0.57721+ds/sv_tree.h
Examining data/vt-0.57721+ds/svm_predict.cpp
Examining data/vt-0.57721+ds/svm_predict.h
Examining data/vt-0.57721+ds/svm_train.cpp
Examining data/vt-0.57721+ds/tbx_ordered_reader.cpp
Examining data/vt-0.57721+ds/tbx_ordered_reader.h
Examining data/vt-0.57721+ds/test.cpp
Examining data/vt-0.57721+ds/test.h
Examining data/vt-0.57721+ds/trio.cpp
Examining data/vt-0.57721+ds/trio.h
Examining data/vt-0.57721+ds/union_variants.cpp
Examining data/vt-0.57721+ds/union_variants.h
Examining data/vt-0.57721+ds/uniq.cpp
Examining data/vt-0.57721+ds/uniq.h
Examining data/vt-0.57721+ds/utils.cpp
Examining data/vt-0.57721+ds/utils.h
Examining data/vt-0.57721+ds/validate.cpp
Examining data/vt-0.57721+ds/validate.h
Examining data/vt-0.57721+ds/variant.cpp
Examining data/vt-0.57721+ds/variant.h
Examining data/vt-0.57721+ds/variant_filter.cpp
Examining data/vt-0.57721+ds/variant_manip.cpp
Examining data/vt-0.57721+ds/variant_manip.h
Examining data/vt-0.57721+ds/version.h
Examining data/vt-0.57721+ds/view.cpp
Examining data/vt-0.57721+ds/view.h
Examining data/vt-0.57721+ds/vntr.cpp
Examining data/vt-0.57721+ds/vntr.h
Examining data/vt-0.57721+ds/vntr_annotator.cpp
Examining data/vt-0.57721+ds/vntr_annotator.h
Examining data/vt-0.57721+ds/vntr_consolidator.cpp
Examining data/vt-0.57721+ds/vntr_extractor.cpp
Examining data/vt-0.57721+ds/vntr_genotyping_record.cpp
Examining data/vt-0.57721+ds/vntr_genotyping_record.h
Examining data/vt-0.57721+ds/vntr_tree.cpp
Examining data/vt-0.57721+ds/vntr_tree.h
Examining data/vt-0.57721+ds/vntrize.cpp
Examining data/vt-0.57721+ds/vntrize.h
Examining data/vt-0.57721+ds/wdp_ahmm.cpp
Examining data/vt-0.57721+ds/wdp_ahmm.h
Examining data/vt-0.57721+ds/bcf_ordered_writer.cpp
Examining data/vt-0.57721+ds/consolidate.h
Examining data/vt-0.57721+ds/discover.h
Examining data/vt-0.57721+ds/estimator.h
Examining data/vt-0.57721+ds/multiallelics_consolidator.h
Examining data/vt-0.57721+ds/svm_train.h
Examining data/vt-0.57721+ds/variant_filter.h
Examining data/vt-0.57721+ds/vntr_consolidator.h
Examining data/vt-0.57721+ds/vntr_extractor.h
Examining data/vt-0.57721+ds/circular_buffer.cpp
Examining data/vt-0.57721+ds/milk_filter.cpp
Examining data/vt-0.57721+ds/normalize.cpp
Examining data/vt-0.57721+ds/paste_genotypes.cpp
Examining data/vt-0.57721+ds/pileup.cpp
Examining data/vt-0.57721+ds/reference_sequence.cpp
Examining data/vt-0.57721+ds/hts_utils.cpp
Examining data/vt-0.57721+ds/hts_utils.h
FINAL RESULTS:
data/vt-0.57721+ds/bam_ordered_reader.cpp:31:12: [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).
strcat(strcpy(fn_list, fn_ref), ".fai");
data/vt-0.57721+ds/bam_ordered_reader.cpp:32:9: [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.
if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
data/vt-0.57721+ds/bam_ordered_reader.cpp:33:13: [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.
if (access(fn_ref, R_OK) == -1) {
data/vt-0.57721+ds/hts_utils.cpp:1477:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/vt-0.57721+ds/hts_utils.cpp:1502:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/vt-0.57721+ds/peek.cpp:725:27: [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.
int32_t sys_ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_afs.cpp:284:23: [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.
int32_t ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_chrom.cpp:270:23: [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.
int32_t ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_fic_hwe.cpp:272:23: [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.
int32_t ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_hwe.cpp:287:23: [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.
int32_t ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_indels.cpp:420:27: [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.
int32_t sys_ret = system(cmd.c_str());
data/vt-0.57721+ds/profile_mendelian.cpp:1267:27: [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.
int32_t sys_ret = system(cmd.c_str());
data/vt-0.57721+ds/bam_ordered_reader.cpp:31:5: [2] (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). Risk is low because the
source is a constant string.
strcat(strcpy(fn_list, fn_ref), ".fai");
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:908:17: [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.
char lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:909:17: [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.
char rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:913:17: [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.
char fuzzy_lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:914:17: [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.
char fuzzy_rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1193:17: [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.
char lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1194:17: [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.
char rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1198:17: [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.
char fuzzy_lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1199:17: [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.
char fuzzy_rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1585:17: [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.
char lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1586:17: [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.
char rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1590:17: [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.
char fuzzy_lflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1591:17: [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.
char fuzzy_rflank_state[3] = {'N', 'N', 'N'};
data/vt-0.57721+ds/consolidate.cpp:497:13: [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 alts[no_alleles];
data/vt-0.57721+ds/consolidate.cpp:734:17: [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.
char alts[no_alleles];
data/vt-0.57721+ds/hts_utils.cpp:272:29: [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).
int32_t count = atoi(token.s);
data/vt-0.57721+ds/hts_utils.cpp:679:16: [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).
file = fopen(alt_hdr_fn.s, "r");
data/vt-0.57721+ds/hts_utils.cpp:821:9: [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(tmp,src,fmt->n);
data/vt-0.57721+ds/hts_utils.cpp:1496:5: [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 buff[255];
data/vt-0.57721+ds/info2tab.cpp:147:19: [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).
out = fopen(output_text_file.c_str(), "w");
data/vt-0.57721+ds/milk_filter.cpp:249:23: [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).
int32_t sex = atoi(ss.substr(idx+1).c_str());
data/vt-0.57721+ds/nuclear_pedigree.cpp:15:110: [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).
addPerson(v[0].c_str(), smIDs, v[2] == "0" ? NULL : v[2].c_str(), v[3] == "0" ? NULL : v[3].c_str(), atoi(v[4].c_str()) );
data/vt-0.57721+ds/peek.cpp:550:21: [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).
FILE *out = fopen(filepath.c_str(), "w");
data/vt-0.57721+ds/profile_afs.cpp:244:21: [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).
FILE *out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_afs.cpp:267:15: [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).
out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_chrom.cpp:215:21: [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).
FILE *out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_chrom.cpp:247:15: [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).
out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_fic_hwe.cpp:232:21: [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).
FILE *out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_fic_hwe.cpp:255:15: [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).
out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_hwe.cpp:226:21: [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).
FILE *out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_hwe.cpp:239:15: [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).
out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_indels.cpp:369:21: [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).
FILE *out = fopen(filepath.c_str(), "w");
data/vt-0.57721+ds/profile_len.cpp:241:21: [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).
FILE *out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_len.cpp:252:15: [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).
out = fopen(file_path.c_str(), "w");
data/vt-0.57721+ds/profile_mendelian.cpp:1169:21: [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).
FILE *out = fopen(filepath.c_str(), "w");
data/vt-0.57721+ds/utils.cpp:230:9: [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 cwd[1024];
data/vt-0.57721+ds/ahmm.cpp:246:12: [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).
mlen = strlen(model[MOTIF]);
data/vt-0.57721+ds/ahmm.cpp:440:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
emission = log10_emission_odds(track_get_base(t), read[j], qual[j]-33);
data/vt-0.57721+ds/ahmm.cpp:457:113: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << emission << " (e: " << (track_get_d(t)<=MOTIF?track_get_base(t):'N') << " vs " << (j!=rlen?read[j]:'N') << ") + ";
data/vt-0.57721+ds/ahmm.cpp:468:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void AHMM::align(const char* read, const char* qual)
data/vt-0.57721+ds/ahmm.cpp:472:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/ahmm.cpp:474:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/ahmm.cpp:474:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/ahmm.cpp:703:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (des_u==D || track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/ahmm.cpp:712:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/ahmm.cpp:904:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(t)==read[j-1])
data/vt-0.57721+ds/ahmm.cpp:1030:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/ahmm.cpp:1115:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j-1];
data/vt-0.57721+ds/ahmm.h:100:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/annotate_indels.cpp:293:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/annotate_indels2.cpp:293:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/annotate_regions.cpp:218:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/annotate_variants.cpp:187:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/annotate_vntrs.cpp:240:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/bam_ordered_reader.cpp:30:30: [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).
fn_list = (char*) calloc(strlen(fn_ref) + 5, 1);
data/vt-0.57721+ds/bam_ordered_reader.cpp:153:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool BAMOrderedReader::read(bam1_t *s)
data/vt-0.57721+ds/bam_ordered_reader.h:100:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(bam1_t *s);
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:124:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/bcf_genotyping_buffered_reader.cpp:1859:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/bcf_ordered_reader.cpp:238:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool BCFOrderedReader::read(bcf1_t *v)
data/vt-0.57721+ds/bcf_ordered_reader.h:112:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(bcf1_t *v);
data/vt-0.57721+ds/bcf_single_genotyping_buffered_reader.cpp:124:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/bcf_single_genotyping_buffered_reader.cpp:163:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/candidate_motif_picker.cpp:69:24: [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).
uint32_t ref_len = strlen(alleles[0]);
data/vt-0.57721+ds/candidate_motif_picker.cpp:74:24: [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).
uint32_t len = strlen(alleles[i]);
data/vt-0.57721+ds/candidate_region_extractor.cpp:139:24: [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).
uint32_t ref_len = strlen(bcf_get_ref(v));
data/vt-0.57721+ds/cat.cpp:213:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/cat.cpp:257:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/chmm.cpp:530:13: [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).
lflen = strlen(model[LFLANK]);
data/vt-0.57721+ds/chmm.cpp:531:12: [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).
mlen = strlen(model[MOTIF]);
data/vt-0.57721+ds/chmm.cpp:532:13: [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).
rflen = strlen(model[RFLANK]);
data/vt-0.57721+ds/chmm.cpp:598:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
emission = log10_emission_odds(track_get_base(t), read[j], qual[j]-33);
data/vt-0.57721+ds/chmm.cpp:615:114: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << emission << " (e: " << (track_get_d(t)<=RFLANK?track_get_base(t):'N') << " vs " << (j!=rlen?read[j]:'N') << ") + ";
data/vt-0.57721+ds/chmm.cpp:626:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void CHMM::align(const char* read, const char* qual, bool debug)
data/vt-0.57721+ds/chmm.cpp:629:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/chmm.cpp:631:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/chmm.cpp:631:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/chmm.cpp:1089:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/chmm.cpp:1343:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(t)==read[j-1])
data/vt-0.57721+ds/chmm.cpp:1482:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/chmm.cpp:1577:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j-1];
data/vt-0.57721+ds/chmm.h:110:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/complex_genotyping_record.cpp:68:16: [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).
dlen = strlen(tmp_alleles[1])-strlen(tmp_alleles[0]);
data/vt-0.57721+ds/complex_genotyping_record.cpp:68:39: [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).
dlen = strlen(tmp_alleles[1])-strlen(tmp_alleles[0]);
data/vt-0.57721+ds/compute_features.cpp:181:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/compute_features2.cpp:183:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/consolidate.cpp:797:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/consolidate_adjacent_vntrs.cpp:103:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (vc->odr->read(v))
data/vt-0.57721+ds/consolidate_vntrs.cpp:103:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (vc->odr->read(v))
data/vt-0.57721+ds/construct_probes.cpp:128:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/decompose.cpp:194:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/decompose2.cpp:172:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/decompose_blocksub.cpp:157:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/decompose_blocksub.cpp:164:30: [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).
size_t ref_len = strlen(allele[0]);
data/vt-0.57721+ds/decompose_blocksub.cpp:165:48: [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).
size_t alt_len = n_allele==1 ? 0 : strlen(allele[1]);
data/vt-0.57721+ds/decompose_blocksub.cpp:282:63: [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).
else if (n_allele==2 && (ref_len!=1) && (ref_len==strlen(allele[1])))
data/vt-0.57721+ds/discover.cpp:1476:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(s))
data/vt-0.57721+ds/estimate.cpp:322:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/filter.cpp:1486:9: [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(exp)!=0)
data/vt-0.57721+ds/filter.cpp:1490:30: [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).
for (uint32_t i=0; i<strlen(exp); ++i)
data/vt-0.57721+ds/filter_overlap.cpp:137:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/fuzzy_partition.cpp:290:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/gencode.cpp:350:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (todr->read(&s))
data/vt-0.57721+ds/genotype.cpp:454:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(s))
data/vt-0.57721+ds/ghmm.cpp:35:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void GHMM::align(const char* ref, const char* read)
data/vt-0.57721+ds/ghmm.cpp:38:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/ghmm.cpp:39:21: [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).
this->len_ref = strlen(ref);
data/vt-0.57721+ds/ghmm.cpp:40:22: [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).
this->len_read = strlen(read);
data/vt-0.57721+ds/ghmm.cpp:40:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->len_read = strlen(read);
data/vt-0.57721+ds/ghmm.cpp:71:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (ref[i - 1] == read[j - 1])
data/vt-0.57721+ds/ghmm.cpp:155:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << ((ref[j++] == read[k++]) ? '|' : ' ');
data/vt-0.57721+ds/ghmm.cpp:174:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j++];
data/vt-0.57721+ds/ghmm.h:50:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/ghmm.h:71:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void set_read(const char * read) {
data/vt-0.57721+ds/ghmm.h:72:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/ghmm.h:78:45: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void align(const char* ref, const char* read);
data/vt-0.57721+ds/hfilter.cpp:171:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/hts_utils.cpp:64:17: [1] (buffer) equal:
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.
return std::equal(ending.rbegin(), ending.rend(), value.rbegin());
data/vt-0.57721+ds/hts_utils.h:472:37: [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).
#define bcf_get_end1(v) ((v)->pos + strlen((v)->d.allele[0]))
data/vt-0.57721+ds/indel_genotyping_record.cpp:51:12: [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).
dlen = strlen(tmp_alleles[1])-strlen(tmp_alleles[0]);
data/vt-0.57721+ds/indel_genotyping_record.cpp:51:35: [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).
dlen = strlen(tmp_alleles[1])-strlen(tmp_alleles[0]);
data/vt-0.57721+ds/info2tab.cpp:264:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/large_motif_tree.cpp:103:20: [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).
uint32_t len = strlen(sequence);
data/vt-0.57721+ds/lfhmm.cpp:290:13: [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).
lflen = strlen(model[LFLANK]);
data/vt-0.57721+ds/lfhmm.cpp:291:12: [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).
mlen = strlen(model[MOTIF]);
data/vt-0.57721+ds/lfhmm.cpp:461:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
emission = log10_emission_odds(track_get_base(t), read[j], qual[j]-33);
data/vt-0.57721+ds/lfhmm.cpp:478:113: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << emission << " (e: " << (track_get_d(t)<=MOTIF?track_get_base(t):'N') << " vs " << (j!=rlen?read[j]:'N') << ") + ";
data/vt-0.57721+ds/lfhmm.cpp:489:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void LFHMM::align(const char* read, const char* qual)
data/vt-0.57721+ds/lfhmm.cpp:493:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/lfhmm.cpp:495:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/lfhmm.cpp:495:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/lfhmm.cpp:791:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (des_u==D || des_u==I || track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/lfhmm.cpp:816:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (des_u==D || track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/lfhmm.cpp:843:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/lfhmm.cpp:1050:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(t)==read[j-1])
data/vt-0.57721+ds/lfhmm.cpp:1189:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/lfhmm.cpp:1272:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j-1];
data/vt-0.57721+ds/lfhmm.h:110:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/lhmm.cpp:199:12: [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).
xlen = strlen(x);
data/vt-0.57721+ds/lhmm.cpp:200:12: [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).
ylen = strlen(y);
data/vt-0.57721+ds/lhmm1.cpp:576:12: [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).
xlen = strlen(x);
data/vt-0.57721+ds/lhmm1.cpp:577:12: [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).
ylen = strlen(y);
data/vt-0.57721+ds/liftover.cpp:209:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/milk_filter.cpp:398:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(nread = 0; odr->read(v); ++nread) {
data/vt-0.57721+ds/multiallelics_consolidator.cpp:207:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/needle.cpp:36:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void NeedlemanWunsch::align(const char* ref, const char* read)
data/vt-0.57721+ds/needle.cpp:39:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/needle.cpp:40:21: [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).
this->len_ref = strlen(ref);
data/vt-0.57721+ds/needle.cpp:41:22: [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).
this->len_read = strlen(read);
data/vt-0.57721+ds/needle.cpp:41:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->len_read = strlen(read);
data/vt-0.57721+ds/needle.cpp:72:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (ref[i - 1] == read[j - 1])
data/vt-0.57721+ds/needle.cpp:156:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << ((ref[j++] == read[k++]) ? '|' : ' ');
data/vt-0.57721+ds/needle.cpp:175:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j++];
data/vt-0.57721+ds/needle.h:49:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/needle.h:65:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void set_read(const char * read)
data/vt-0.57721+ds/needle.h:67:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/needle.h:73:45: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void align(const char* ref, const char* read);
data/vt-0.57721+ds/normalize.cpp:188:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:99:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:140:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:220:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:333:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:406:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_bcf_overlap_matcher.cpp:443:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/ordered_region_overlap_matcher.cpp:56:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (todr->read(&s))
data/vt-0.57721+ds/ordered_region_overlap_matcher.cpp:90:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (todr->read(&s))
data/vt-0.57721+ds/paste.cpp:181:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (odrs[i]->read(vs[i]))
data/vt-0.57721+ds/paste_and_compute_features_sequential.cpp:270:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while( odr->read(v) ) {
data/vt-0.57721+ds/paste_and_compute_features_sequential.cpp:357:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ( ! odr->read(v) ) {
data/vt-0.57721+ds/paste_and_compute_features_sequential.cpp:449:27: [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 ( p_dp[0] != strlen(p_st[0]) ) {
data/vt-0.57721+ds/paste_genotypes.cpp:275:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while( odr->read(v) ) {
data/vt-0.57721+ds/paste_genotypes.cpp:375:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ( !odr->read(v) ) {
data/vt-0.57721+ds/paste_genotypes.cpp:469:25: [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).
if ( p_dp[0] != strlen(p_st[0]) ) {
data/vt-0.57721+ds/peek.cpp:207:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/pregex.cpp:97:22: [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).
subject_length = strlen((char *)subject);
data/vt-0.57721+ds/profile_afs.cpp:150:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_chrom.cpp:143:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_fic_hwe.cpp:150:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_hwe.cpp:154:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_len.cpp:155:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_mendelian.cpp:346:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/profile_vntrs.cpp:247:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/rfhmm.cpp:316:12: [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).
mlen = strlen(model[MOTIF]);
data/vt-0.57721+ds/rfhmm.cpp:317:13: [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).
rflen = strlen(model[RFLANK]);
data/vt-0.57721+ds/rfhmm.cpp:488:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
emission = log10_emission_odds(track_get_base(t), read[j], qual[j]-33);
data/vt-0.57721+ds/rfhmm.cpp:505:114: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << emission << " (e: " << (track_get_d(t)<=RFLANK?track_get_base(t):'N') << " vs " << (j!=rlen?read[j]:'N') << ") + ";
data/vt-0.57721+ds/rfhmm.cpp:516:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void RFHMM::align(const char* read, const char* qual)
data/vt-0.57721+ds/rfhmm.cpp:520:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/rfhmm.cpp:522:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/rfhmm.cpp:522:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/rfhmm.cpp:759:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/rfhmm.cpp:816:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/rfhmm.cpp:1003:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(t)==read[j-1])
data/vt-0.57721+ds/rfhmm.cpp:1133:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/rfhmm.cpp:1228:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j-1];
data/vt-0.57721+ds/rfhmm.h:116:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/rfhmm_x.cpp:316:12: [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).
mlen = strlen(model[MOTIF]);
data/vt-0.57721+ds/rfhmm_x.cpp:317:13: [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).
rflen = strlen(model[RFLANK]);
data/vt-0.57721+ds/rfhmm_x.cpp:488:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
emission = log10_emission_odds(track_get_base(t), read[j], qual[j]-33);
data/vt-0.57721+ds/rfhmm_x.cpp:505:114: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << emission << " (e: " << (track_get_d(t)<=RFLANK?track_get_base(t):'N') << " vs " << (j!=rlen?read[j]:'N') << ") + ";
data/vt-0.57721+ds/rfhmm_x.cpp:528:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void RFHMM_X::align(const char* read, const char* qual)
data/vt-0.57721+ds/rfhmm_x.cpp:532:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/rfhmm_x.cpp:534:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/rfhmm_x.cpp:534:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/rfhmm_x.cpp:854:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/rfhmm_x.cpp:911:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(des_t)!=read[j-1])
data/vt-0.57721+ds/rfhmm_x.cpp:1098:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (track_get_base(t)==read[j-1])
data/vt-0.57721+ds/rfhmm_x.cpp:1228:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/rfhmm_x.cpp:1323:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << read[j-1];
data/vt-0.57721+ds/rfhmm_x.h:116:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
data/vt-0.57721+ds/rminfo.cpp:132:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/set_ref.cpp:182:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/sort.cpp:159:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/sort.cpp:194:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/sort.cpp:223:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/subset.cpp:168:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/svm_predict.cpp:127:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(odr->read(v))
data/vt-0.57721+ds/tbx_ordered_reader.cpp:147:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool TBXOrderedReader::read(kstring_t *s)
data/vt-0.57721+ds/tbx_ordered_reader.h:104:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(kstring_t *s);
data/vt-0.57721+ds/test.cpp:406:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (todr.read(&s))
data/vt-0.57721+ds/utils.cpp:33:26: [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).
for (uint32_t i=0; i<strlen(delims); ++i)
data/vt-0.57721+ds/utils.cpp:80:26: [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).
for (uint32_t i=0; i<strlen(delims); ++i)
data/vt-0.57721+ds/utils.cpp:90:30: [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).
int32_t i=0, lastIndex = strlen(str)-1;
data/vt-0.57721+ds/validate.cpp:132:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/validate.cpp:164:31: [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).
int32_t len = strlen(alleles[0]);
data/vt-0.57721+ds/variant.cpp:223:20: [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).
int32_t rlen = strlen(ref);
data/vt-0.57721+ds/variant.cpp:238:26: [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).
size_t len = strlen(allele[i]);
data/vt-0.57721+ds/variant.cpp:318:28: [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).
int32_t alen = strlen(alt);
data/vt-0.57721+ds/variant_manip.cpp:66:21: [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).
uint32_t rlen = strlen(vcf_ref);
data/vt-0.57721+ds/variant_manip.cpp:125:16: [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).
rlen = strlen(alleles[0]);
data/vt-0.57721+ds/variant_manip.cpp:126:16: [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).
alen = strlen(alleles[1]);
data/vt-0.57721+ds/variant_manip.cpp:168:23: [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).
len = strlen(alleles[i]);
data/vt-0.57721+ds/variant_manip.cpp:177:23: [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).
len = strlen(alleles[0]);
data/vt-0.57721+ds/variant_manip.cpp:249:20: [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).
int32_t rlen = strlen(ref);
data/vt-0.57721+ds/variant_manip.cpp:264:26: [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).
size_t len = strlen(allele[i]);
data/vt-0.57721+ds/variant_manip.cpp:344:28: [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).
int32_t alen = strlen(alt);
data/vt-0.57721+ds/view.cpp:191:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/vntr_extractor.cpp:256:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/vntrize.cpp:191:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (odr->read(v))
data/vt-0.57721+ds/wdp_ahmm.cpp:278:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void WDP_AHMM::align(const char* read, const char* qual)
data/vt-0.57721+ds/wdp_ahmm.cpp:282:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
this->read = read;
data/vt-0.57721+ds/wdp_ahmm.cpp:284:12: [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).
rlen = strlen(read);
data/vt-0.57721+ds/wdp_ahmm.cpp:284:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rlen = strlen(read);
data/vt-0.57721+ds/wdp_ahmm.cpp:803:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << "read : " << read << "\n";
data/vt-0.57721+ds/wdp_ahmm.h:64:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read;
ANALYSIS SUMMARY:
Hits = 257
Lines analyzed = 82415 in approximately 2.03 seconds (40569 lines/second)
Physical Source Lines of Code (SLOC) = 51883
Hits@level = [0] 985 [1] 209 [2] 36 [3] 0 [4] 12 [5] 0
Hits@level+ = [0+] 1242 [1+] 257 [2+] 48 [3+] 12 [4+] 12 [5+] 0
Hits/KSLOC@level+ = [0+] 23.9385 [1+] 4.95345 [2+] 0.925159 [3+] 0.23129 [4+] 0.23129 [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.