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/phast-1.5+dfsg/include/bd_phylo_hmm.h
Examining data/phast-1.5+dfsg/include/bed.h
Examining data/phast-1.5+dfsg/include/bgc_hmm.h
Examining data/phast-1.5+dfsg/include/category_map.h
Examining data/phast-1.5+dfsg/include/complex.h
Examining data/phast-1.5+dfsg/include/complex_matrix.h
Examining data/phast-1.5+dfsg/include/complex_vector.h
Examining data/phast-1.5+dfsg/include/dgamma.h
Examining data/phast-1.5+dfsg/include/eigen.h
Examining data/phast-1.5+dfsg/include/em.h
Examining data/phast-1.5+dfsg/include/fit_column.h
Examining data/phast-1.5+dfsg/include/fit_em.h
Examining data/phast-1.5+dfsg/include/fit_feature.h
Examining data/phast-1.5+dfsg/include/gap_patterns.h
Examining data/phast-1.5+dfsg/include/genepred.h
Examining data/phast-1.5+dfsg/include/gff.h
Examining data/phast-1.5+dfsg/include/hashtable.h
Examining data/phast-1.5+dfsg/include/hmm.h
Examining data/phast-1.5+dfsg/include/indel_history.h
Examining data/phast-1.5+dfsg/include/indel_mod.h
Examining data/phast-1.5+dfsg/include/list_of_lists.h
Examining data/phast-1.5+dfsg/include/lists.h
Examining data/phast-1.5+dfsg/include/local_alignment.h
Examining data/phast-1.5+dfsg/include/maf.h
Examining data/phast-1.5+dfsg/include/maf_block.h
Examining data/phast-1.5+dfsg/include/markov_matrix.h
Examining data/phast-1.5+dfsg/include/matrix.h
Examining data/phast-1.5+dfsg/include/memory_handler.h
Examining data/phast-1.5+dfsg/include/misc.h
Examining data/phast-1.5+dfsg/include/motif.h
Examining data/phast-1.5+dfsg/include/ms.h
Examining data/phast-1.5+dfsg/include/msa.h
Examining data/phast-1.5+dfsg/include/multi_msa.h
Examining data/phast-1.5+dfsg/include/numerical_opt.h
Examining data/phast-1.5+dfsg/include/pbs_code.h
Examining data/phast-1.5+dfsg/include/phast_cons.h
Examining data/phast-1.5+dfsg/include/phylo_fit.h
Examining data/phast-1.5+dfsg/include/phylo_hmm.h
Examining data/phast-1.5+dfsg/include/phylo_p.h
Examining data/phast-1.5+dfsg/include/phylo_p_print.h
Examining data/phast-1.5+dfsg/include/prob_matrix.h
Examining data/phast-1.5+dfsg/include/prob_vector.h
Examining data/phast-1.5+dfsg/include/pssm.h
Examining data/phast-1.5+dfsg/include/puzzler.h
Examining data/phast-1.5+dfsg/include/queues.h
Examining data/phast-1.5+dfsg/include/rph_util.h
Examining data/phast-1.5+dfsg/include/simplex_grid.h
Examining data/phast-1.5+dfsg/include/stacks.h
Examining data/phast-1.5+dfsg/include/stringsplus.h
Examining data/phast-1.5+dfsg/include/subst_distrib.h
Examining data/phast-1.5+dfsg/include/subst_mods.h
Examining data/phast-1.5+dfsg/include/sufficient_stats.h
Examining data/phast-1.5+dfsg/include/tfbs.h
Examining data/phast-1.5+dfsg/include/tree_likelihoods.h
Examining data/phast-1.5+dfsg/include/tree_model.h
Examining data/phast-1.5+dfsg/include/trees.h
Examining data/phast-1.5+dfsg/include/vector.h
Examining data/phast-1.5+dfsg/include/wig.h
Examining data/phast-1.5+dfsg/include/external_libs.h
Examining data/phast-1.5+dfsg/src/dless/bd_phylo_hmm.c
Examining data/phast-1.5+dfsg/src/dless/dless.c
Examining data/phast-1.5+dfsg/src/dless/dlessP.c
Examining data/phast-1.5+dfsg/src/exoniphy/exoniphy.c
Examining data/phast-1.5+dfsg/src/lib/base/complex_matrix.c
Examining data/phast-1.5+dfsg/src/lib/base/complex_vector.c
Examining data/phast-1.5+dfsg/src/lib/base/eigen.c
Examining data/phast-1.5+dfsg/src/lib/base/hashtable.c
Examining data/phast-1.5+dfsg/src/lib/base/list_of_lists.c
Examining data/phast-1.5+dfsg/src/lib/base/lists.c
Examining data/phast-1.5+dfsg/src/lib/base/markov_matrix.c
Examining data/phast-1.5+dfsg/src/lib/base/matrix.c
Examining data/phast-1.5+dfsg/src/lib/base/memory_handler.c
Examining data/phast-1.5+dfsg/src/lib/base/misc.c
Examining data/phast-1.5+dfsg/src/lib/base/numerical_opt.c
Examining data/phast-1.5+dfsg/src/lib/base/prob_matrix.c
Examining data/phast-1.5+dfsg/src/lib/base/prob_vector.c
Examining data/phast-1.5+dfsg/src/lib/base/stringsplus.c
Examining data/phast-1.5+dfsg/src/lib/base/vector.c
Examining data/phast-1.5+dfsg/src/lib/feature/bed.c
Examining data/phast-1.5+dfsg/src/lib/feature/category_map.c
Examining data/phast-1.5+dfsg/src/lib/feature/genepred.c
Examining data/phast-1.5+dfsg/src/lib/feature/gff.c
Examining data/phast-1.5+dfsg/src/lib/feature/wig.c
Examining data/phast-1.5+dfsg/src/lib/hmm/em.c
Examining data/phast-1.5+dfsg/src/lib/hmm/hmm.c
Examining data/phast-1.5+dfsg/src/lib/motif/motif.c
Examining data/phast-1.5+dfsg/src/lib/motif/tfbs.c
Examining data/phast-1.5+dfsg/src/lib/msa/local_alignment.c
Examining data/phast-1.5+dfsg/src/lib/msa/maf.c
Examining data/phast-1.5+dfsg/src/lib/msa/maf_block.c
Examining data/phast-1.5+dfsg/src/lib/msa/msa.c
Examining data/phast-1.5+dfsg/src/lib/msa/multi_msa.c
Examining data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c
Examining data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c
Examining data/phast-1.5+dfsg/src/lib/phylo/dgamma.c
Examining data/phast-1.5+dfsg/src/lib/phylo/fit_column.c
Examining data/phast-1.5+dfsg/src/lib/phylo/fit_em.c
Examining data/phast-1.5+dfsg/src/lib/phylo/fit_feature.c
Examining data/phast-1.5+dfsg/src/lib/phylo/indel_history.c
Examining data/phast-1.5+dfsg/src/lib/phylo/indel_mod.c
Examining data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c
Examining data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c
Examining data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c
Examining data/phast-1.5+dfsg/src/lib/phylo/phylo_p_print.c
Examining data/phast-1.5+dfsg/src/lib/phylo/subst_distrib.c
Examining data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c
Examining data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c
Examining data/phast-1.5+dfsg/src/lib/phylo/tree_model.c
Examining data/phast-1.5+dfsg/src/lib/phylo/trees.c
Examining data/phast-1.5+dfsg/src/lib/phylo_hmm/gap_patterns.c
Examining data/phast-1.5+dfsg/src/lib/phylo_hmm/phylo_hmm.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_bgc_hmm.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_category_map.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_gff.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_hmm.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_list_of_lists.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_phastCons.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_phyloP.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_phylo_hmm.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_subst_mods.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_tree_model.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_util.c
Examining data/phast-1.5+dfsg/src/lib/rphast/rph_wig.c
Examining data/phast-1.5+dfsg/src/phastCons/phastCons.c
Examining data/phast-1.5+dfsg/src/phastMotif/phastMotif.c
Examining data/phast-1.5+dfsg/src/phastOdds/phastOdds.c
Examining data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c
Examining data/phast-1.5+dfsg/src/phyloFit/phyloFit.c
Examining data/phast-1.5+dfsg/src/phyloP/phyloP.c
Examining data/phast-1.5+dfsg/src/prequel/pbs_code.c
Examining data/phast-1.5+dfsg/src/prequel/simplex_grid.c
Examining data/phast-1.5+dfsg/src/prequel/pbsDecode.c
Examining data/phast-1.5+dfsg/src/prequel/pbsEncode.c
Examining data/phast-1.5+dfsg/src/prequel/pbsScoreMatrix.c
Examining data/phast-1.5+dfsg/src/prequel/pbsTrain.c
Examining data/phast-1.5+dfsg/src/prequel/prequel.c
Examining data/phast-1.5+dfsg/src/util/phast.c
Examining data/phast-1.5+dfsg/src/util/all_dists.c
Examining data/phast-1.5+dfsg/src/util/base_evolve.c
Examining data/phast-1.5+dfsg/src/util/chooseLines.c
Examining data/phast-1.5+dfsg/src/util/clean_genes.c
Examining data/phast-1.5+dfsg/src/util/consEntropy.c
Examining data/phast-1.5+dfsg/src/util/convert_coords.c
Examining data/phast-1.5+dfsg/src/util/display_rate_matrix.c
Examining data/phast-1.5+dfsg/src/util/draw_tree.c
Examining data/phast-1.5+dfsg/src/util/eval_predictions.c
Examining data/phast-1.5+dfsg/src/util/hmm_train.c
Examining data/phast-1.5+dfsg/src/util/hmm_tweak.c
Examining data/phast-1.5+dfsg/src/util/hmm_view.c
Examining data/phast-1.5+dfsg/src/util/indelFit.c
Examining data/phast-1.5+dfsg/src/util/indelHistory.c
Examining data/phast-1.5+dfsg/src/util/maf_parse.c
Examining data/phast-1.5+dfsg/src/util/makeHKY.c
Examining data/phast-1.5+dfsg/src/util/modFreqs.c
Examining data/phast-1.5+dfsg/src/util/msa_diff.c
Examining data/phast-1.5+dfsg/src/util/msa_split.c
Examining data/phast-1.5+dfsg/src/util/msa_view.c
Examining data/phast-1.5+dfsg/src/util/phastBias.c
Examining data/phast-1.5+dfsg/src/util/refeature.c
Examining data/phast-1.5+dfsg/src/util/stringiphy.c
Examining data/phast-1.5+dfsg/src/util/treeGen.c
Examining data/phast-1.5+dfsg/src/util/tree_doctor.c
FINAL RESULTS:
data/phast-1.5+dfsg/include/hashtable.h:98:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(keycpy, key);
data/phast-1.5+dfsg/include/misc.h:335:8: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#undef printf
data/phast-1.5+dfsg/include/misc.h:336:9: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define printf Rprintf
data/phast-1.5+dfsg/include/misc.h:351:8: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#undef fprintf
data/phast-1.5+dfsg/include/misc.h:352:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define fprintf rphast_fprintf
data/phast-1.5+dfsg/src/dless/dlessP.c:328:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s/%s.html", htmldir, id->chars);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:217:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(extrapolate_tree_fname,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:220:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(extrapolate_tree_fname,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:285:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s\\exoniphy\\mammals\\%s", data_path->chars, default_hmm);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:287:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s/exoniphy/mammals/%s", data_path->chars, default_hmm);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:309:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s\\exoniphy\\%s-gc%d", data_path->chars,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:312:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s/exoniphy/%s-gc%d", data_path->chars,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:326:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s\\exoniphy\\mammals\\%s", data_path->chars, str->chars);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:328:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s/exoniphy/mammals/%s", data_path->chars, str->chars);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:338:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s\\exoniphy\\%s", data_path->chars,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:341:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s/exoniphy/%s", data_path->chars,
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:466:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s.v%d.gff", sens_spec_fname_root, trial+1);
data/phast-1.5+dfsg/src/lib/base/hashtable.c:59:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(keycpy, key);
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:38:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tempname, name);
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:120:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tempstr, val);
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:144:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tempstr, vals[i]);
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:53:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(M->states, states);
data/phast-1.5+dfsg/src/lib/base/matrix.c:136:7: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(F, formatstr, m->data[i][j]);
data/phast-1.5+dfsg/src/lib/base/misc.c:226:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(file_alph, line->chars);
data/phast-1.5+dfsg/src/lib/base/misc.c:227:29: [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).
if (!predefined_alph) strcpy(alph, line->chars);
data/phast-1.5+dfsg/src/lib/base/misc.c:311:3: [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, warnfmt, args);
data/phast-1.5+dfsg/src/lib/base/misc.c:322:3: [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, warnfmt, args);
data/phast-1.5+dfsg/src/lib/base/misc.c:351:15: [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.
else return vfprintf(f, format, args);
data/phast-1.5+dfsg/src/lib/base/misc.c:472:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(retval, word);
data/phast-1.5+dfsg/src/lib/base/misc.c:1108:10: [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.
return (access(filename, F_OK) == 0);
data/phast-1.5+dfsg/src/lib/base/vector.c:81:5: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(F, formatstr, v->data[i]);
data/phast-1.5+dfsg/src/lib/feature/bed.c:64:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(group, "id \"%s.%d\"", bed_name->chars, num);
data/phast-1.5+dfsg/src/lib/feature/bed.c:68:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(group, "id \"%s\"", bed_name->chars);
data/phast-1.5+dfsg/src/lib/feature/category_map.c:638:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(groupstr, "%s \"%s.%d\"", grouptag != NULL ? grouptag : "id",
data/phast-1.5+dfsg/src/lib/feature/category_map.c:641:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(groupstr, "%s \"%d\"", grouptag != NULL ? grouptag : "id", groupno);
data/phast-1.5+dfsg/src/lib/feature/category_map.c:673:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(groupstr, "%s \"%s.%d\"", grouptag != NULL ? grouptag : "id",
data/phast-1.5+dfsg/src/lib/feature/category_map.c:676:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(groupstr, "%s \"%d\"", grouptag != NULL ? grouptag : "id",
data/phast-1.5+dfsg/src/lib/feature/genepred.c:95:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(group, "transcript_id \"%s.%d\"", name->chars, num);
data/phast-1.5+dfsg/src/lib/feature/genepred.c:99:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(group, "transcript_id \"%s\"", name->chars);
data/phast-1.5+dfsg/src/lib/feature/gff.c:687:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, ".*%s[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)", tag);
data/phast-1.5+dfsg/src/lib/feature/gff.c:912:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s \"%d\"", tag, idx);
data/phast-1.5+dfsg/src/lib/feature/gff.c:914:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s \"%s.%d\"", tag, group->name->chars, idx);
data/phast-1.5+dfsg/src/lib/feature/gff.c:1159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp, "gene_id \"%s\" ; %s", g->name->chars, f->attribute != NULL ?
data/phast-1.5+dfsg/src/lib/feature/wig.c:58:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(chromVal, val->chars);
data/phast-1.5+dfsg/src/lib/feature/wig.c:91:26: [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).
if (chrom != NULL) strcpy(chrom, chromVal);
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:158:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while (fscanf(F, "%s ", tag) != EOF) {
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:52:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ms->alphabet, alphabet);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:56:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ms->alphabet, DEFAULT_ALPHABET);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:273:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ms->names[i], n->chars);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:485:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(outfile, formatstr, firstChar, sub->src->chars,
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:503:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(outfile, formatstr, sub->src->chars,
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:511:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(outfile, formatstr, sub->src->chars);
data/phast-1.5+dfsg/src/lib/msa/msa.c:79:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->alphabet, alphabet);
data/phast-1.5+dfsg/src/lib/msa/msa.c:83:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->alphabet, DEFAULT_ALPHABET);
data/phast-1.5+dfsg/src/lib/msa/msa.c:144:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->names[i], tmpstr->chars);
data/phast-1.5+dfsg/src/lib/msa/msa.c:151:16: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if (1 != fscanf(F, "%s", msa->names[i]))
data/phast-1.5+dfsg/src/lib/msa/msa.c:161:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->names[i], &line[j]);
data/phast-1.5+dfsg/src/lib/msa/msa.c:319:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->names[i], n->chars);
data/phast-1.5+dfsg/src/lib/msa/msa.c:1449:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(names[i][j], msa->names[j]);
data/phast-1.5+dfsg/src/lib/msa/msa.c:2809:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->alphabet, newalph);
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:568:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msa->names[i+1], axtfname->chars); /* ?? */
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:78:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tempstr, "%s:%s", foregd_branch, "bgc[0,]");
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:238:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(warning_str, "WARNING: Pruned away leaves of tree with no match in alignment (%s",
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:241:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:242:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(warning_str, "%s)\n", warning_str);
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:354:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outfn, "%s.%s.mod", b->mods_fn, bgchmm_get_state_name(i, do_bgc));
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:96:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp_mod_fname, "fit_em.%s.%d.mod", tmpstr, getpid());
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:455:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cons_fname, "%s.cons.mod", estim_trees_fname_root);
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:456:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(noncons_fname, "%s.noncons.mod", estim_trees_fname_root);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:124:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(rv[i], tempstr2);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:154:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(rv[idx++], n->name);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:168:25: [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).
if (prefix != NULL) strcpy(rv[state], prefix);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:185:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(rv[i], tempch);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:751:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpchstr, "(%s,%s)", msa->names[0], msa->names[1]);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:756:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpchstr, "(%s,(%s,%s))", msa->names[0], msa->names[1],
data/phast-1.5+dfsg/src/lib/phylo/phylo_p_print.c:706:6: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(outfile, (formatstr == NULL ? "%.5f" : formatstr[col]), data[col][tup]);
data/phast-1.5+dfsg/src/lib/phylo/phylo_p_print.c:809:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(outfile, (formatstr == NULL ? "%.5f" : formatstr[col]), data[col][i]);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2685:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alphabet, mm->states);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:382:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while (fscanf(f, "%s", tag) != EOF) {
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:522:19: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while (EOF != fscanf(f, "%s", tag)) {
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:3998:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tempch, "%s#%i", fore ? foreground : "backgd", cat);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:4009:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tempch, ",%s#%i", fore1 ? foreground : "backgd", cat1);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:269:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(str, n->name);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:272:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(str, n->name);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:276:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(str, temp);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:279:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(temp, " # %s", n->label);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:280:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(str, temp);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:442:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest->name, src->name);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:1389:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(n->name, repname[n->lchild->id]);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:1391:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(n->name, repname[n->rchild->id]);
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:76:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(names[i], CHAR(STRING_ELT(namesP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:85:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqs[i], CHAR(STRING_ELT(seqsP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:92:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alphabet, CHARACTER_VALUE(alphabetP));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:317:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alphabet, CHARACTER_VALUE(alphabetP));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:371:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(&cmStr[cmStrLen], "; %s %i", CHAR(STRING_ELT(docatsP, i)), i+1);
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:1075:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(temp, "id \"%s\"", names[currstate]);
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:1085:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(temp, "id \"%s\"", names[currstate]);
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c:130:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(pf->subtree_name, CHARACTER_VALUE(scaleSubtreeP));
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c:168:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(&temp[pos], "%s", CHARACTER_VALUE(STRING_ELT(noOptP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloP.c:65:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tempstr, CHARACTER_VALUE(methodP));
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloP.c:74:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tempstr, CHARACTER_VALUE(modeP));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:71:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(names[i], CHAR(STRING_ELT(namesP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:80:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqs[i], CHAR(STRING_ELT(seqsP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:87:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alphabet, CHARACTER_VALUE(alphabetP));
data/phast-1.5+dfsg/src/lib/rphast/rph_tree_model.c:432:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(alphabet, CHARACTER_VALUE(alphabetP));
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:76:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(strvec[numtrees], currStr);
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:217:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(str, CHAR(STRING_ELT(newNamesP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:229:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(n->name, str);
data/phast-1.5+dfsg/src/phastCons/phastCons.c:267:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(p->extrapolate_tree_fname,
data/phast-1.5+dfsg/src/phastCons/phastCons.c:270:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(p->extrapolate_tree_fname,
data/phast-1.5+dfsg/src/phastCons/phastCons.c:289:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp, "%s\\data\\phastCons\\%s", PHAST_HOME,
data/phast-1.5+dfsg/src/phastCons/phastCons.c:292:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp, "%s/data/phastCons/%s", PHAST_HOME,
data/phast-1.5+dfsg/src/phastCons/phastCons.c:301:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp, "%s\\data\\exoniphy\\mammals\\r3.ncns.mod, %s\\data\\exoniphy\\mammals\\r3.cns.mod, %s\\data\\exoniphy\\mammals\\r3.cds-1.mod, %s\\data\\exoniphy\\mammals\\r3.cds-2.mod, %s\\data\\exoniphy\\mammals\\r3.cds-3.mod", PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME);
data/phast-1.5+dfsg/src/phastCons/phastCons.c:303:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp, "\
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:60:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(descriptions[mod->bl_idx+idx],
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:74:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(descriptions[mod->backgd_idx + i], "background freq(%s)", tempstr);
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:102:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(descriptions[mod->ratematrix_idx+i], str->chars);
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:330:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpchstr, "(%s,%s)", msa->names[0], msa->names[1]);
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:334:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpchstr, "(%s,(%s,%s))", msa->names[0], msa->names[1],
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:414:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fname, "%s.%d.%s", dump_msas_root, i+1,
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:472:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fname, "%s.%d.mod", dump_mods_root, i+1);
data/phast-1.5+dfsg/src/prequel/pbsTrain.c:158:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(comment, "# Code generated by pbsTrain, with argument(s) \"%s\"\n\
data/phast-1.5+dfsg/src/prequel/prequel.c:180:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out_fname, "%s.stats", out_root);
data/phast-1.5+dfsg/src/prequel/prequel.c:203:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out_fname, "%s.%s.probs", out_root, n->name);
data/phast-1.5+dfsg/src/prequel/prequel.c:253:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out_fname, "%s.%s.fa", out_root, n->name);
data/phast-1.5+dfsg/src/prequel/prequel.c:285:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out_fname, "%s.%s.bin", out_root, n->name);
data/phast-1.5+dfsg/src/util/clean_genes.c:556:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(str12, str1); strcat(str12, str2);
data/phast-1.5+dfsg/src/util/clean_genes.c:556:23: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcpy(str12, str1); strcat(str12, str2);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:616:4: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(rate_format_string, val);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:705:7: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(rate_format_string, vec_get(model->backgd_freqs, i));
data/phast-1.5+dfsg/src/util/maf_parse.c:189:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fname, "%s.%s.maf", out_root, name->chars);
data/phast-1.5+dfsg/src/util/maf_parse.c:338:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(splitFormat, "%%s%%.%si.%%s", optarg);
data/phast-1.5+dfsg/src/util/maf_parse.c:508:2: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(outfilename, splitFormat, out_root_fname, ++blockIdx,
data/phast-1.5+dfsg/src/util/msa_split.c:832:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(subfname, "%s.%d-%d.%s", out_fname_root, orig_start,
data/phast-1.5+dfsg/src/util/msa_split.c:867:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(subfname, "%s.%d-%d.gff", out_fname_root, orig_start, orig_end);
data/phast-1.5+dfsg/src/util/msa_split.c:910:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(subfname, "%s.%s-%d.%s", out_fname_root,
data/phast-1.5+dfsg/src/util/stringiphy.c:58:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmpstr, "%s \"%s\"", gene_tag, gene_val);
data/phast-1.5+dfsg/src/util/treeGen.c:191:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(root->lchild->name, name1);
data/phast-1.5+dfsg/src/util/treeGen.c:194:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(root->rchild->name, name2);
data/phast-1.5+dfsg/src/util/treeGen.c:220:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(newleaf->name, lname);
data/phast-1.5+dfsg/src/util/treeGen.c:252:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(newleaf->name, lname);
data/phast-1.5+dfsg/src/util/tree_doctor.c:202:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(optarg, "%s\\data\\exoniphy\\mammals\\cftr25_hybrid.nh",
data/phast-1.5+dfsg/src/util/tree_doctor.c:205:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(optarg, "%s/data/exoniphy/mammals/cftr25_hybrid.nh",
data/phast-1.5+dfsg/src/util/tree_doctor.c:350:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(n->name, newname);
data/phast-1.5+dfsg/include/misc.h:196:5: [3] (random) random:
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.
int random();
data/phast-1.5+dfsg/include/misc.h:197:6: [3] (random) srandom:
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.
void srandom(int seed);
data/phast-1.5+dfsg/include/misc.h:369:30: [3] (random) random:
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.
#define unif_rand(void) (1.0*random()/RAND_MAX)
data/phast-1.5+dfsg/src/dless/dless.c:73:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "R:t:p:E:C:r:M:i:N:P:I:H:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/dless/dlessP.c:68:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "r:M:i:t:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:110:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "i:D:c:H:m:s:p:g:B:T:L:F:IW:N:n:b:e:A:xSYUhq",
data/phast-1.5+dfsg/src/lib/base/misc.c:53:3: [3] (random) srandom:
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.
srandom((unsigned int)time(NULL));
data/phast-1.5+dfsg/src/lib/base/misc.c:74:5: [3] (random) random:
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.
int random()
data/phast-1.5+dfsg/src/lib/base/misc.c:79:6: [3] (random) srandom:
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.
void srandom(int seed)
data/phast-1.5+dfsg/src/lib/base/misc.c:81:3: [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(seed);
data/phast-1.5+dfsg/src/lib/base/misc.c:94:3: [3] (random) srandom:
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.
srandom((unsigned int)time(NULL));
data/phast-1.5+dfsg/src/lib/base/misc.c:330:5: [3] (random) srandom:
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.
srandom((unsigned int)now.tv_usec);
data/phast-1.5+dfsg/src/lib/base/misc.c:331:10: [3] (random) srandom:
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.
} else srandom(seed);
data/phast-1.5+dfsg/src/phastCons/phastCons.c:81:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv,
data/phast-1.5+dfsg/src/phastMotif/phastMotif.c:150:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "t:i:b:sk:md:pn:I:R:P:w:c:SB:o:HDxh")) != -1) {
data/phast-1.5+dfsg/src/phastOdds/phastOdds.c:64:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "B:b:F:f:r:g:w:W:i:ydvh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:170:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "L:n:i:d:a:m:o:xR:qht:s:k:Ep:M:S:w:l:P:F:D:r",
data/phast-1.5+dfsg/src/phyloFit/phyloFit.c:102:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "m:t:s:g:c:C:i:o:k:a:l:w:v:M:p:A:I:K:S:b:d:O:u:Y:e:D:GVENRqLPXZUBFfnrzhWyJ", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/phyloP/phyloP.c:56:3: [3] (random) srandom:
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.
srandom((unsigned int)now.tv_usec);
data/phast-1.5+dfsg/src/phyloP/phyloP.c:59:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "m:o:i:n:pc:s:f:Fe:l:r:B:d:qwgbPN:h",
data/phast-1.5+dfsg/src/prequel/pbsDecode.c:35:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:e:Gh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/prequel/pbsEncode.c:39:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "Gh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/prequel/pbsScoreMatrix.c:38:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "a:b:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/prequel/pbsTrain.c:58:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "n:b:l:Gxh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/prequel/prequel.c:53:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "r:i:s:e:knxSh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/all_dists.c:61:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "mt:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/base_evolve.c:50:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "n:o:f:c:e:s:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/chooseLines.c:36:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "k:rh")) != -1) {
data/phast-1.5+dfsg/src/util/clean_genes.c:1015:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "N:i:r:L:M:S:g:d:stlnfceICxh",
data/phast-1.5+dfsg/src/util/consEntropy.c:63:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "H:N::h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/convert_coords.c:61:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "hm:f:s:d:i:p:n:")) != -1) {
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:393:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "t:fedlLiM:N:A:B:aszSECh")) != -1) {
data/phast-1.5+dfsg/src/util/draw_tree.c:46:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "dbvsh")) != -1) {
data/phast-1.5+dfsg/src/util/eval_predictions.c:232:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "r:p:f:l:d:n:h")) != -1) {
data/phast-1.5+dfsg/src/util/hmm_train.c:126:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "i:g:c:m:M:R:I:n:t:P:G:qh")) != -1) {
data/phast-1.5+dfsg/src/util/hmm_tweak.c:96:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "m:a:e:f:t:i:u:F:T:zyRh")) != -1) {
data/phast-1.5+dfsg/src/util/hmm_view.c:54:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "k:i:t:C:xh")) != -1) {
data/phast-1.5+dfsg/src/util/indelFit.c:56:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "a:b:t:Lcf:r:l:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/indelHistory.c:44:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "i:H:AIh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/maf_parse.c:314:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:e:l:O:r:S:d:g:c:P:b:o:m:M:pLnxEIh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/makeHKY.c:42:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "g:p:t:T:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/modFreqs.c:29:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/msa_diff.c:41:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "bga:i:j:h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/msa_split.c:453:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "i:M:g:c:p:d:n:sfG:r:o:L:C:T:w:I:O:B:P:F:l:xSzqh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/msa_view.c:465:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "i:o:s:e:l:G:r:T:a:g:c:C:L:I:A:M:O:w:N:Y:X:fuDVxPzRSk4mh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/phastBias.c:73:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "B:b:L:l:C:c:R:E:T:S:s:f:g:p:m:i:oWh", long_opts, &opt_idx))
data/phast-1.5+dfsg/src/util/refeature.c:142:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "o:i:l:g:e:d:UISfusbh", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/stringiphy.c:74:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/treeGen.c:35:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "h", long_opts, &opt_idx)) != -1) {
data/phast-1.5+dfsg/src/util/tree_doctor.c:192:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:p:P:g:m:r:R:B:S:D:l:L:adtNbnh",
data/phast-1.5+dfsg/include/lists.h:78:5: [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(&l->array[i * l->step], o, l->elementsz);
data/phast-1.5+dfsg/include/maf_block.h:39:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char lineType[4]; /**< type of line i, either 's', 'q', 'i', 'e' */
data/phast-1.5+dfsg/include/maf_block.h:40:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char iStatus[2]; /**< leftStatus and rightStatus; only defined if
data/phast-1.5+dfsg/include/trees.h:47:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */
data/phast-1.5+dfsg/src/dless/dlessP.c:319:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[STR_MED_LEN];
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:106:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[STR_LONG_LEN];
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:465:7: [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 tmpstr[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:160:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "%i", i);
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:168:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "%i", i);
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:244:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char **names, **src, **feature, **strand, **attribute, tempStrand[2];
data/phast-1.5+dfsg/src/lib/base/lists.c:100:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(lastelement, lst_get(l, lst_size(l)-1), l->elementsz);
data/phast-1.5+dfsg/src/lib/base/lists.c:195:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(tmp, lst_get(l, j), l->elementsz);
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:181:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[2*MAXALPHA], *states;
data/phast-1.5+dfsg/src/lib/base/misc.c:208:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char file_alph[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/base/misc.c:286:7: [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).
F = fopen(fname, mode);
data/phast-1.5+dfsg/src/lib/base/misc.c:1215:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BUFFERSIZE];
data/phast-1.5+dfsg/src/lib/base/numerical_opt.c:922:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[30];
data/phast-1.5+dfsg/src/lib/base/numerical_opt.c:926:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "x_%d", i);
data/phast-1.5+dfsg/src/lib/base/numerical_opt.c:930:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "df/dx_%d", i);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:36:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:37:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "%d", i);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:42:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:43:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "%f", d);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:93:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:94:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "%d", i);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:100:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[(int)ceil(log10(d)) + 1 + 10];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:101:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "%.9f", d);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:143:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BUFFERSIZE];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:184:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BUFFERSIZE];
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:239:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BUFFERSIZE];
data/phast-1.5+dfsg/src/lib/feature/bed.c:26:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char group[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/feature/bed.c:73:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(group, "id \"bed.%d\"", id++);
data/phast-1.5+dfsg/src/lib/feature/category_map.c:478:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fname[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/feature/category_map.c:490:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(fname, "cm.tmp.%d", getpid());
data/phast-1.5+dfsg/src/lib/feature/category_map.c:622:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char groupstr[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/feature/genepred.c:30:5: [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 group[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/feature/gff.c:405:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char score_str[50], frame_str[50];
data/phast-1.5+dfsg/src/lib/feature/gff.c:408:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(score_str, "%.3f", feat->score);
data/phast-1.5+dfsg/src/lib/feature/gff.c:411:8: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(frame_str, "%d", (3 - feat->frame) % 3);
data/phast-1.5+dfsg/src/lib/feature/gff.c:877:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/feature/gff.c:1151:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[STR_LONG_LEN];
data/phast-1.5+dfsg/src/lib/feature/wig.c:32:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chromVal[STR_LONG_LEN];
data/phast-1.5+dfsg/src/lib/feature/wig.c:105:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chrom[STR_LONG_LEN];
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:154:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tag[100];
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:723:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[50];
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:734:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpstr, "-INF");
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:736:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "%.3f", emission_scores[i][j]);
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:751:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpstr, "-INF");
data/phast-1.5+dfsg/src/lib/hmm/hmm.c:753:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "%.3f", full_scores[i][j]);
data/phast-1.5+dfsg/src/lib/motif/motif.c:887:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[tuple_size+1];
data/phast-1.5+dfsg/src/lib/motif/motif.c:939:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuple[tuple_size + 1];
data/phast-1.5+dfsg/src/lib/motif/motif.c:1676:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cons[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:450:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bases[4] = {'A','C','G','T'};
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:473:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(str, "%f", num);
data/phast-1.5+dfsg/src/lib/msa/maf.c:327:5: [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 tuple_str[msa->nseqs * tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/maf.c:332:5: [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 reftuple[tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/maf.c:694:5: [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 tuple_str[msa->nseqs * tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/maf.c:699:5: [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 reftuple[tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:120:16: [2] (integer) atol:
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).
sub->start = atol(((String*)lst_get_ptr(l, 2))->chars);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:123:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sub->size = atoi(((String*)lst_get_ptr(l, 3))->chars);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:134:18: [2] (integer) atol:
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).
sub->srcSize = atol(((String*)lst_get_ptr(l, 5))->chars);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:199:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sub->iCount[i] = atoi(str->chars);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:429:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempstr[1000];
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:442:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%li", sub->start);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:447:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%i", sub->size);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:454:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%li", sub->srcSize);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:467:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char firstChar, formatstr[1000];
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:483:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(formatstr, "%%c %%-%is %%%ii %%%ii %%c %%%ii ",
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:501:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(formatstr, "i %%-%is %%c %%i %%c %%i",
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:510:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(formatstr, "q %%-%is", fieldSize[1]);
data/phast-1.5+dfsg/src/lib/msa/msa.c:148:5: [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 line[MAX_LINE_LEN];
data/phast-1.5+dfsg/src/lib/msa/msa.c:237:5: [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(retval->categories, msa->categories, msa->length * sizeof(int));
data/phast-1.5+dfsg/src/lib/msa/msa.c:447:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char **seq, codon[3], key[msa->nseqs * 3 + 1];
data/phast-1.5+dfsg/src/lib/msa/msa.c:1661:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cod[4], *codon_mapping = get_codon_mapping(msa->alphabet);
data/phast-1.5+dfsg/src/lib/msa/msa.c:2023:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp_codon[3];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:79:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char key[msa->nseqs * tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:610:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[ss->tuple_size * msa->nseqs + (ss->tuple_size-1) + 1];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1041:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char new_tuple[msa->ss->tuple_size * msa->nseqs + 1];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1153:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[msa->nseqs * ts];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1211:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char key[msa->nseqs * msa->ss->tuple_size + 1];
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1389:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char base[2];
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:53:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempstr[1000];
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:235:5: [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 warning_str[10000];
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:352:5: [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 outfn[1000];
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:383:5: [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 tempname[1000];
data/phast-1.5+dfsg/src/lib/phylo/bgc_hmm.c:390:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempname, "random.path.%i", i+1);
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:60:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp_mod_fname[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:92:5: [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 tmpstr[20];
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:94:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpstr, "phast");
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:367:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[30];
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:371:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "x_%d", i);
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:394:5: [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 cons_fname[STR_MED_LEN], noncons_fname[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:578:2: [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 temp[100];
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:585:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp, "state.%i", j);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:119:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempstr2[100];
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:122:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr2, "rate.cat.%i", i);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:145:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(rv[idx++], "nsite");
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:178:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempch[100];
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:183:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempch, "%i", i+1);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:231:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuplestr[mod->order+2];
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:232:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char coltupstr[msa->nseqs+1];
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:636:2: [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 temp[100];
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:637:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp, "GC%i", i);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:672:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpchstr[STR_MED_LEN];
data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c:356:4: [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 str[1000];
data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c:357:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(str, "#neutral mean = %.3f var = %.3f\n#post_mean post_var pval",
data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c:424:11: [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 str[1000];
data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c:425:11: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(str, "#neutral mean_sub = %.3f var_sub = %.3f mean_sup = %.3f var_sup = %.3f\n#post_mean_sub post_var_sub post_mean_sup post_var_sup pval",
data/phast-1.5+dfsg/src/lib/phylo/phylo_p.c:649:5: [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 *formatstr[4] = {"%.3f", "%.3f", "%.3f", "%.0f"};
data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c:486:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuple[mod->order + 2];
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:368:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tag[STR_MED_LEN], alphabet[MAX_ALPH_SIZE];
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:848:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cat = atoi(((String*)lst_get_ptr(templst, 1))->chars);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:931:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sharemod = atoi(((String*)lst_get_ptr(templst, 1))->chars);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:2521:16: [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).
int val = atoi(((String*)lst_get_ptr(tmplst, 1))->chars);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:3921:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempch[10000];
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:4022:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempch, "bgc#%i", bgcmod);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:4029:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempch, "sel#%i", selmod[selpar]);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:259:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/phast-1.5+dfsg/src/lib/phylo/trees.c:275:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp, ":%g", n->dparent);
data/phast-1.5+dfsg/src/lib/rphast/rph_gff.c:72:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char strandStr[2];
data/phast-1.5+dfsg/src/lib/rphast/rph_gff.c:74:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gffCols[9][20] = {"seqname", "src", "feature", "start", "end", "score", "strand", "frame", "attribute"};
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:368:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cmStr, "NCATS = %i", LENGTH(docatsP));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:1063:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp, "state%i", i+1);
data/phast-1.5+dfsg/src/lib/rphast/rph_phastCons.c:129:5: [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 tempstr[100];
data/phast-1.5+dfsg/src/lib/rphast/rph_phastCons.c:133:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%i", intp[i]-1);
data/phast-1.5+dfsg/src/lib/rphast/rph_phastCons.c:139:5: [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 tempstr[100];
data/phast-1.5+dfsg/src/lib/rphast/rph_phastCons.c:143:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%i", intp[i]-1);
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloP.c:55:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempstr[1000];
data/phast-1.5+dfsg/src/lib/rphast/rph_phylo_hmm.c:89:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tempstr[100];
data/phast-1.5+dfsg/src/lib/rphast/rph_phylo_hmm.c:94:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tempstr, "%i", intp[i]-1);
data/phast-1.5+dfsg/src/phastCons/phastCons.c:283:5: [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 tmp[5000];
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:42:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(descriptions[mod->scale_idx], "tree scale");
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:44:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(descriptions[mod->scale_idx+1], "subtree scale");
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:57:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(descriptions[mod->bl_idx+idx], "branch (spans root)");
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:63:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(descriptions[mod->bl_idx+idx],
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:81:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(descriptions[mod->ratevar_idx+i], "alpha");
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:83:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(descriptions[mod->ratevar_idx+i], "rate var #%d", i+1);
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:89:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(descriptions[mod->ratematrix_idx], "kappa");
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:97:9: [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 tmp[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:98:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, " (%d,%d)", lst_get_int(rows, j) + 1,
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:132:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fname[STR_MED_LEN];
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:133:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpchstr[STR_MED_LEN];
data/phast-1.5+dfsg/src/prequel/pbsTrain.c:31:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comment[1000];
data/phast-1.5+dfsg/src/prequel/pbs_code.c:551:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char bytes[MAX_NBYTES];
data/phast-1.5+dfsg/src/prequel/pbs_code.c:570:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char bytes[MAX_NBYTES];
data/phast-1.5+dfsg/src/prequel/prequel.c:29:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char out_fname[STR_MED_LEN];
data/phast-1.5+dfsg/src/util/chooseLines.c:39:11: [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).
k = atoi(optarg);
data/phast-1.5+dfsg/src/util/chooseLines.c:58:5: [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 tmpstr[20];
data/phast-1.5+dfsg/src/util/chooseLines.c:59:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "choose_lines.%d", getpid());
data/phast-1.5+dfsg/src/util/clean_genes.c:178:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuplestr[4];
data/phast-1.5+dfsg/src/util/clean_genes.c:182:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * start_signal[1] = { "ATG" };
data/phast-1.5+dfsg/src/util/clean_genes.c:204:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuplestr[4];
data/phast-1.5+dfsg/src/util/clean_genes.c:208:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * stop_signals[3] = { "TAA", "TAG", "TGA" };
data/phast-1.5+dfsg/src/util/clean_genes.c:233:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuplestr[3];
data/phast-1.5+dfsg/src/util/clean_genes.c:237:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * splice_signals[3] = {"GT", "GC", "AT"};
data/phast-1.5+dfsg/src/util/clean_genes.c:262:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuplestr[3];
data/phast-1.5+dfsg/src/util/clean_genes.c:266:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * splice_signals[2] = {"AG", "AC"};
data/phast-1.5+dfsg/src/util/clean_genes.c:279:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seq[feat->end - feat->start + 2];
data/phast-1.5+dfsg/src/util/clean_genes.c:521:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str1[3], str2[3], str12[5];
data/phast-1.5+dfsg/src/util/clean_genes.c:524:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * splice_pairs[3] = {"GTAG", "GCAG", "ATAC"};
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:176:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuple_i[mod_tuples->order+1], tuple_j[mod_tuples->order+1];
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:204:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuple_i[mod->order+2], tuple_j[mod->order+2];
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:387:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tuple[5], tuple2[5]; /* , aa_alph[50]; */
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:523:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((F = fopen(subst_mat_fname, "r")) == NULL) {
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:529:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((F = fopen(subst_mat_fname_paml, "r")) == NULL) {
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:535:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((F = fopen(subst_score_fname, "r")) == NULL) {
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:541:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((F = fopen(order1_mod_fname, "r")) == NULL) {
data/phast-1.5+dfsg/src/util/maf_parse.c:270:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[1000], splitFormat[100]="%s%.1i.maf", *group_tag = NULL;
data/phast-1.5+dfsg/src/util/maf_parse.c:332:23: [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).
splitInterval = atoi(optarg);
data/phast-1.5+dfsg/src/util/maf_parse.c:362:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
base_mask_cutoff = atoi(optarg);
data/phast-1.5+dfsg/src/util/makeHKY.c:31:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[50];
data/phast-1.5+dfsg/src/util/makeHKY.c:86:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmpstr, "(s1:%f,s2:%f)", t/2, t/2);
data/phast-1.5+dfsg/src/util/msa_split.c:283:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[STR_MED_LEN];
data/phast-1.5+dfsg/src/util/msa_split.c:294:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "(%d)", length_strip);
data/phast-1.5+dfsg/src/util/msa_split.c:300:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "(%d)", nallgaps_strip);
data/phast-1.5+dfsg/src/util/msa_split.c:306:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(tmp, "(%d)", nanygaps_strip);
data/phast-1.5+dfsg/src/util/msa_split.c:420:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char subfname[STR_MED_LEN];
data/phast-1.5+dfsg/src/util/msa_view.c:869:9: [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 name[STR_SHORT_LEN];
data/phast-1.5+dfsg/src/util/msa_view.c:870:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(name, "%d-%d", i, i+win_size-1);
data/phast-1.5+dfsg/src/util/stringiphy.c:55:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpstr[STR_LONG_LEN];
data/phast-1.5+dfsg/include/hashtable.h:97:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
keycpy = (char*)smalloc(sizeof(char) * (strlen(key) + 1));
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:201:25: [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).
data_path = str_new(strlen(PHAST_HOME)+strlen("/data")+1);
data/phast-1.5+dfsg/src/exoniphy/exoniphy.c:201:44: [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).
data_path = str_new(strlen(PHAST_HOME)+strlen("/data")+1);
data/phast-1.5+dfsg/src/lib/base/hashtable.c:58:33: [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).
keycpy = smalloc(sizeof(char)*(strlen(key)+1));
data/phast-1.5+dfsg/src/lib/base/hashtable.c:74:5: [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.
int equal(void *key1ptr, void *key2) {
data/phast-1.5+dfsg/src/lib/base/hashtable.c:88:61: [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.
(idx = lst_find_compare(ht->keys[bucket], (void*)key, equal)) == -1)
data/phast-1.5+dfsg/src/lib/base/hashtable.c:105:61: [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.
(idx = lst_find_compare(ht->keys[bucket], (void*)key, equal)) == -1)
data/phast-1.5+dfsg/src/lib/base/hashtable.c:118:61: [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.
(idx = lst_find_compare(ht->keys[bucket], (void*)key, equal)) == -1)
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:37:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tempname = smalloc((strlen(name)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:119:22: [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).
tempstr = smalloc((strlen(val)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/base/list_of_lists.c:143:24: [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).
tempstr = smalloc((strlen(vals[i])+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:40:44: [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).
alph_size = states == NULL ? size : (int)strlen(states);
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:186:35: [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).
states = smalloc(sizeof(char) * strlen(line));
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:187:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0; i < strlen(line); i++) {
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:585:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(labels) != backgd->size) die("mm_sample_backgd: got num_labels=%i but backgd->size=%i\n", strlen(labels), backgd->size);
data/phast-1.5+dfsg/src/lib/base/markov_matrix.c:585:104: [1] (buffer) strlen:
Does not handle 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(labels) != backgd->size) die("mm_sample_backgd: got num_labels=%i but backgd->size=%i\n", strlen(labels), backgd->size);
data/phast-1.5+dfsg/src/lib/base/misc.c:121:24: [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).
int alph_size = (int)strlen(alphabet);
data/phast-1.5+dfsg/src/lib/base/misc.c:167:25: [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).
int tuple_size = (int)strlen(tuple);
data/phast-1.5+dfsg/src/lib/base/misc.c:182:38: [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).
int k, remainder, alph_size = (int)strlen(alphabet);
data/phast-1.5+dfsg/src/lib/base/misc.c:206:25: [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).
int predefined_alph = strlen(alph) == 0 ? 0 : 1;
data/phast-1.5+dfsg/src/lib/base/misc.c:228:24: [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).
file_size = (int)strlen(file_alph);
data/phast-1.5+dfsg/src/lib/base/misc.c:229:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size = (int)strlen(alph);
data/phast-1.5+dfsg/src/lib/base/misc.c:470:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = (int)strlen(word);
data/phast-1.5+dfsg/src/lib/base/misc.c:1161:23: [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).
for (j = 0; j < strlen(iupac_map[i]); j++) {
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:30:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
String *s = str_new((int)strlen(str));
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:85:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
str_nappend_charstr(s, charstr, (int)strlen(charstr));
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:448:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = (int)strlen(substr);
data/phast-1.5+dfsg/src/lib/base/stringsplus.c:460:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = (int)strlen(substr);
data/phast-1.5+dfsg/src/lib/feature/gff.c:407:28: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
if (feat->score_is_null) strcpy(score_str, ".");
data/phast-1.5+dfsg/src/lib/feature/gff.c:410:38: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
if (feat->frame == GFF_NULL_FRAME) strcpy(frame_str, ".");
data/phast-1.5+dfsg/src/lib/feature/gff.c:669:29: [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).
char *tmpstr=smalloc((100+strlen(tag))*sizeof(char));
data/phast-1.5+dfsg/src/lib/feature/gff.c:676:24: [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).
int i, taglen = (int)strlen(tag);
data/phast-1.5+dfsg/src/lib/motif/motif.c:99:31: [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).
alph_size = multiseq ? (int)strlen(pmsa->pooled_msa->alphabet) :
data/phast-1.5+dfsg/src/lib/motif/motif.c:100:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(int)strlen(seqset->set->alphabet);
data/phast-1.5+dfsg/src/lib/motif/motif.c:300:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (sample < 0 || position < 0) return (int)strlen(set->alphabet);
data/phast-1.5+dfsg/src/lib/motif/motif.c:883:24: [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).
int alph_size = (int)strlen(s->set->alphabet);
data/phast-1.5+dfsg/src/lib/motif/motif.c:947:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tuple, &s->set->seqs[i][start], tuple_size);
data/phast-1.5+dfsg/src/lib/motif/motif.c:1009:35: [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).
int alph_size = multiseq ? (int)strlen(pmsa->pooled_msa->alphabet) :
data/phast-1.5+dfsg/src/lib/motif/motif.c:1010:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(int)strlen(ss->set->alphabet);
data/phast-1.5+dfsg/src/lib/motif/motif.c:1247:23: [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).
m->alph_size = (int)strlen(m->alphabet);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:51:36: [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).
ms->alphabet = (char*)smalloc((strlen(alphabet) + 1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:55:36: [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).
ms->alphabet = (char*)smalloc((strlen(DEFAULT_ALPHABET)+1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:110:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seqLen = (int)strlen(ms->seqs[i]);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:322:20: [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).
alph_size = (int)strlen(inputMS->alphabet);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:329:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seqLen = (int)strlen(inputMS->seqs[j]);
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:358:23: [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).
for (i = (int)strlen(inputMS->seqs[j]); i >= 0 ; i--) {
data/phast-1.5+dfsg/src/lib/motif/tfbs.c:700:21: [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 = 0; j < strlen(ms->seqs[i]); j++)
data/phast-1.5+dfsg/src/lib/msa/maf.c:142:30: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:142:52: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:145:30: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:145:52: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:330:26: [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).
int alph_size = (int)strlen(msa->alphabet), nreftuples = int_pow(alph_size, tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf.c:406:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reftuple, &refseq->chars[i-tuple_size+1], tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf.c:422:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(msa->ss->col_tuples[tuple_idx], tuple_str, msa->nseqs * tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf.c:597:30: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, msa->length);
data/phast-1.5+dfsg/src/lib/msa/maf.c:597:52: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, msa->length);
data/phast-1.5+dfsg/src/lib/msa/maf.c:603:30: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, 50000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:603:52: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, 50000);
data/phast-1.5+dfsg/src/lib/msa/maf.c:697:26: [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).
int alph_size = (int)strlen(msa->alphabet), nreftuples = int_pow(alph_size, tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf.c:762:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reftuple, &refseq->chars[i-tuple_size+1], tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf.c:777:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(msa->ss->col_tuples[tuple_idx], tuple_str, msa->nseqs * tuple_size);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:443:9: [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(tempstr) > fieldSize[2])
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:444:27: [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).
fieldSize[2] = (int)strlen(tempstr);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:448:9: [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(tempstr) > fieldSize[3])
data/phast-1.5+dfsg/src/lib/msa/maf_block.c: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).
fieldSize[3] = (int)strlen(tempstr);
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:455:9: [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(tempstr) > fieldSize[5])
data/phast-1.5+dfsg/src/lib/msa/maf_block.c:456:27: [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).
fieldSize[5] = (int)strlen(tempstr);
data/phast-1.5+dfsg/src/lib/msa/msa.c:78:37: [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).
msa->alphabet = (char*)smalloc((strlen(alphabet) + 1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/msa/msa.c:82:37: [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).
msa->alphabet = (char*)smalloc((strlen(DEFAULT_ALPHABET)+1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/msa/msa.c:522:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new_msa->ss->col_tuples[idx], key, (msa->nseqs*tuple_size+1));
data/phast-1.5+dfsg/src/lib/msa/msa.c:557:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->seqs != NULL) msa->length = (unsigned int)strlen(msa->seqs[0]);
data/phast-1.5+dfsg/src/lib/msa/msa.c:1448:37: [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).
names[i][j] = (char*)smalloc((strlen(msa->names[j]) + 1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/msa/msa.c:1481:21: [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 = 0; i < strlen(msa->alphabet); i++)
data/phast-1.5+dfsg/src/lib/msa/msa.c:1495:21: [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 = 0; i < strlen(msa->alphabet); i++) {
data/phast-1.5+dfsg/src/lib/msa/msa.c:1513:25: [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).
int i, j, size = (int)strlen(msa->alphabet);
data/phast-1.5+dfsg/src/lib/msa/msa.c:1590:24: [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).
int alph_size = (int)strlen(msa->alphabet);
data/phast-1.5+dfsg/src/lib/msa/msa.c:1660:46: [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).
int i, j, spec, numcodon, alph_size = (int)strlen(msa->alphabet);
data/phast-1.5+dfsg/src/lib/msa/msa.c:2294:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(names[i], s->chars, STR_SHORT_LEN);
data/phast-1.5+dfsg/src/lib/msa/msa.c:2350:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(source_msa->names[j], names[j], STR_SHORT_LEN);
data/phast-1.5+dfsg/src/lib/msa/msa.c:2670:26: [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 (i = 0, j = 0; i < strlen(msa->alphabet); i++)
data/phast-1.5+dfsg/src/lib/msa/msa.c:2806:24: [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).
int i, nchars = (int)strlen(newalph);
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:120:30: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+ (int)strlen(msa->missing) + 1,
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:120:58: [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).
max_tuples = pow_bounded(strlen(msa->alphabet)+ (int)strlen(msa->missing) + 1,
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:142:32: [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).
max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:142:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:169:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(main_ss->col_tuples[idx], source_ss->col_tuples[i],
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:202:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(key, smsa->ss->col_tuples[smsa->ss->tuple_idx[i]],
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:219:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(main_ss->col_tuples[idx], key, msa->nseqs * tuple_size);
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:383:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(key, smsa->ss->col_tuples[j], (smsa->nseqs * tuple_size + 1));
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1138:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(ss->col_tuples[new_tuple_idx], new_tuple,
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1157:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tmp, msa->ss->col_tuples[tup], msa->nseqs * ts);
data/phast-1.5+dfsg/src/lib/msa/sufficient_stats.c:1219:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(key, msa->ss->col_tuples[i], (msa->nseqs * msa->ss->tuple_size + 1));
data/phast-1.5+dfsg/src/lib/phylo/fit_em.c:417:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:225:9: [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(msa->missing) < 2)
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:226:46: [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).
die("ERROR strlen(msa->missing)=%i\n", strlen(msa->missing));
data/phast-1.5+dfsg/src/lib/phylo/phast_cons.c:1130:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(mod->rate_matrix->states) != 4 ||
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:123:22: [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).
rv[i] = smalloc((strlen(tempstr2)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:153:24: [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).
rv[idx] = smalloc((strlen(n->name)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:164:25: [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).
else prefixlen = (int)strlen(prefix);
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:184:22: [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).
rv[i] = smalloc((strlen(tempch)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/phylo/phylo_fit.c:594:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(n->name) > 0)
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:249:14: [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).
n = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:252:14: [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).
n = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:895:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:938:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1029:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1064:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1143:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1190:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1291:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1330:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1420:33: [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).
int i, j, k, alph_size = (int)strlen(mod->rate_matrix->states), codi[3], codj[3],
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1503:22: [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).
alph_size = (int)strlen(states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1574:22: [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).
alph_size = (int)strlen(states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1767:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1791:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1847:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1874:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1934:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:1963:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2031:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2064:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2123:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2206:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2230:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2249:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2302:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2350:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2378:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2443:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2467:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2521:17: [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).
nstate = (int)strlen(states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2542:17: [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).
nstate = (int)strlen(states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2654:24: [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).
int i, nstate = (int)strlen(states);
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2672:22: [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).
alph_size = (int)strlen(mm->states), chartype[5];
data/phast-1.5+dfsg/src/lib/phylo/subst_mods.c:2683:30: [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).
alphabet = smalloc(((int)strlen(mm->states)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c:47:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c:484:37: [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).
int i, seq, idx, alph_size = (int)strlen(msa->alphabet);
data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c:844:24: [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).
int alph_size = (int)strlen(alphabet);
data/phast-1.5+dfsg/src/lib/phylo/tree_likelihoods.c:889:25: [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).
int tuple_size = (int)strlen(tuple);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:79:27: [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).
nstate = int_pow((int)strlen(alphabet), tm->order+1);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:586:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0; i < strlen(tm->rate_matrix->states); i++)
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:2102:25: [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).
nstate = int_pow((int)strlen(msa[0]->alphabet), mod[0]->order+1);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:2556:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currparam->length = (int)strlen(currparam->chars);
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:3229:21: [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).
int numstate=(int)strlen(msa->alphabet), **minState, *numMinState;
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:3492:30: [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).
Vector *aa_freqs = vec_new(strlen(AA_ALPHABET));
data/phast-1.5+dfsg/src/lib/phylo/tree_model.c:3493:33: [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).
MarkovMatrix *aa_mat = mm_new(strlen(AA_ALPHABET), AA_ALPHABET, CONTINUOUS);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:63:58: [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).
int i, in_distance = FALSE, in_label=FALSE, len = (int)strlen(treestr), nopen_parens = 0,
data/phast-1.5+dfsg/src/lib/phylo/trees.c:142:9: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(node->name, &c, 1);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:252:24: [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).
str = srealloc(str, (strlen(str)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/phylo/trees.c:264:5: [1] (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 character.
strcat(str, "(");
data/phast-1.5+dfsg/src/lib/phylo/trees.c:266:5: [1] (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 character.
strcat(str, ",");
data/phast-1.5+dfsg/src/lib/phylo/trees.c:268:5: [1] (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 character.
strcat(str, ")");
data/phast-1.5+dfsg/src/lib/phylo/trees.c:291:14: [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).
len = (int)strlen(root->name);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:788:26: [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).
xoffset = -3 * strlen(n->name);
data/phast-1.5+dfsg/src/lib/phylo/trees.c:1390:2: [1] (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 character.
strcat(n->name, "-");
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:75:27: [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).
names[i] = smalloc((strlen(CHAR(STRING_ELT(namesP, i)))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:84:26: [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).
seqs[i] = smalloc((strlen(CHAR(STRING_ELT(seqsP, i)))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:91:25: [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).
alphabet = smalloc((strlen(CHARACTER_VALUE(alphabetP))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:129:22: [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).
int i, alph_size = strlen(msa->alphabet);
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:316:25: [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).
alphabet = smalloc((strlen(CHARACTER_VALUE(alphabetP))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:366:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmStrLen += strlen(CHAR(STRING_ELT(docatsP, i))) + 10;
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:370:23: [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).
cmStrLen = (int)strlen(cmStr);
data/phast-1.5+dfsg/src/lib/rphast/rph_msa.c:1213:25: [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).
nstate = int_pow((int)strlen(msa->alphabet), mod->order+1);
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c:129:35: [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).
pf->subtree_name = smalloc((1+strlen(CHARACTER_VALUE(scaleSubtreeP)))*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c:164:14: [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).
len += strlen(CHARACTER_VALUE(STRING_ELT(noOptP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_phyloFit.c:169:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pos += strlen(CHARACTER_VALUE(STRING_ELT(noOptP, i)));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:70:27: [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).
names[i] = smalloc((strlen(CHAR(STRING_ELT(namesP, i)))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:79:26: [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).
seqs[i] = smalloc((strlen(CHAR(STRING_ELT(seqsP, i)))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:86:25: [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).
alphabet = smalloc((strlen(CHARACTER_VALUE(alphabetP))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:215:26: [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).
totalSeqLengths += strlen(inputMS->seqs[i]);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:332:27: [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).
outputNseqs += ceil(strlen(inputMS->seqs[inputSeqNum]) / (double)windowSize);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:347:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
while ((strlen(inputMS->seqs[inputSeqNum])-nextCutAt) > windowSize)
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:350:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputMS->names[outputSeqNum] = (char*)smalloc((strlen(inputMS->names[inputSeqNum])+1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:351:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:351:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:352:41: [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).
outputMS->names[outputSeqNum][strlen(inputMS->names[inputSeqNum])] = '\0';
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:356:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->seqs[outputSeqNum], inputMS->seqs[inputSeqNum] + nextCutAt, windowSize);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:367:12: [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).
if ((strlen(inputMS->seqs[inputSeqNum])-nextCutAt) > 0)
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:370:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outputMS->names[outputSeqNum] = (char*)smalloc((strlen(inputMS->names[inputSeqNum])+1) * sizeof(char*));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:371:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:371:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(outputMS->names[outputSeqNum], inputMS->names[inputSeqNum], strlen(inputMS->names[inputSeqNum]));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:372:41: [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).
outputMS->names[outputSeqNum][strlen(inputMS->names[inputSeqNum])] = '\0';
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:375:25: [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).
inputSeqLen = strlen(inputMS->seqs[inputSeqNum]);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:377:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->seqs[outputSeqNum], inputMS->seqs[inputSeqNum] + nextCutAt, inputSeqLen-nextCutAt);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:475:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((feature->start > 0) && ((feature->start-1+ lengthOfSubSequence) <= strlen(inputMS->seqs[currentSequence]))) {
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:479:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->seqs[outputSeqNum], inputMS->seqs[currentSequence] + (feature->start-1), lengthOfSubSequence);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:700:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(inputMS->seqs[currentSequence]), inputMS->idx_offsets[currentSequence],
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:701:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(inputMS->alphabet), MarkovMatrices, pwm, reverseCompPWM,
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:754:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(inputMS->seqs[currentSequence]), inputMS->idx_offsets[currentSequence],
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:755:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(inputMS->alphabet), MarkovMatrices, pwm, reverseCompPWM,
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:812:42: [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).
outputMS->names[i] = (char*)smalloc((strlen(name)+1) * sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:813:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->names[i], name, strlen(name));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:813:39: [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).
strncpy(outputMS->names[i], name, strlen(name));
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:814:24: [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).
outputMS->names[i][strlen(name)] = '\0';
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:818:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(outputMS->seqs[i], seq, length[i]);
data/phast-1.5+dfsg/src/lib/rphast/rph_tfbs.c:913:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
resultP[i] = strlen(ms->seqs[i]);
data/phast-1.5+dfsg/src/lib/rphast/rph_tree_model.c:431:23: [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).
alphabet = smalloc((strlen(CHARACTER_VALUE(alphabetP))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_tree_model.c:439:17: [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).
dim = int_pow(strlen(alphabet), tm_order(subst_mod)+1);
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:52:20: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (';'!=(c=fgetc(infile))) {
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:75:35: [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).
strvec[numtrees] = smalloc((strlen(currStr)+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:216:20: [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).
str = smalloc((strlen(CHAR(STRING_ELT(newNamesP, i)))+1)*sizeof(char));
data/phast-1.5+dfsg/src/lib/rphast/rph_trees.c:344:9: [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(node->name)==0 || strcmp(node->name, ";")==0)
data/phast-1.5+dfsg/src/phastCons/phastCons.c:265:42: [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).
p->extrapolate_tree_fname = smalloc((strlen(PHAST_HOME)+100)*sizeof(char));
data/phast-1.5+dfsg/src/phastMotif/phastMotif.c:338:35: [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).
backgd_mnmod = vec_new((int)strlen(seqset->set->alphabet));
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:59:11: [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 (strlen(n->name) > 0)
data/phast-1.5+dfsg/src/phyloBoot/phyloBoot.c:527:11: [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 (strlen(descriptions[j]) < 1)
data/phast-1.5+dfsg/src/util/clean_genes.c:164:21: [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 = 0; j < strlen(signals[i]); j++) {
data/phast-1.5+dfsg/src/util/consEntropy.c:95:22: [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).
alph_size = (int)strlen(cons_mod->rate_matrix->states);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:75:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:93:24: [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).
int alph_size = (int)strlen(mod->rate_matrix->states);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:127:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int size = (int)strlen(paml_alph);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:175:24: [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).
int alph_size = (int)strlen(mod_tuples->rate_matrix->states);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:203:24: [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).
int alph_size = (int)strlen(alph);
data/phast-1.5+dfsg/src/util/display_rate_matrix.c:519:20: [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).
alph_size = (int)strlen(model->rate_matrix->states);
data/phast-1.5+dfsg/src/util/maf_parse.c:188:26: [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).
char *fname = smalloc((strlen(out_root)+name->length+7)*sizeof(char));
data/phast-1.5+dfsg/src/util/msa_split.c:258:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0; i < strlen(alphabet); i++) {
data/phast-1.5+dfsg/src/util/msa_split.c:285:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (j = 0; j < strlen(alphabet); j++) {
ANALYSIS SUMMARY:
Hits = 592
Lines analyzed = 80534 in approximately 2.61 seconds (30842 lines/second)
Physical Source Lines of Code (SLOC) = 52856
Hits@level = [0] 985 [1] 218 [2] 180 [3] 50 [4] 144 [5] 0
Hits@level+ = [0+] 1577 [1+] 592 [2+] 374 [3+] 194 [4+] 144 [5+] 0
Hits/KSLOC@level+ = [0+] 29.8358 [1+] 11.2002 [2+] 7.07583 [3+] 3.67035 [4+] 2.72438 [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.