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/kma-1.3.7/align.c
Examining data/kma-1.3.7/align.h
Examining data/kma-1.3.7/alnfrags.c
Examining data/kma-1.3.7/alnfrags.h
Examining data/kma-1.3.7/ankers.c
Examining data/kma-1.3.7/ankers.h
Examining data/kma-1.3.7/assembly.c
Examining data/kma-1.3.7/assembly.h
Examining data/kma-1.3.7/chain.c
Examining data/kma-1.3.7/chain.h
Examining data/kma-1.3.7/compdna.c
Examining data/kma-1.3.7/compdna.h
Examining data/kma-1.3.7/compkmers.c
Examining data/kma-1.3.7/compkmers.h
Examining data/kma-1.3.7/compress.c
Examining data/kma-1.3.7/compress.h
Examining data/kma-1.3.7/db.c
Examining data/kma-1.3.7/db.h
Examining data/kma-1.3.7/decon.c
Examining data/kma-1.3.7/decon.h
Examining data/kma-1.3.7/dist.c
Examining data/kma-1.3.7/dist.h
Examining data/kma-1.3.7/ef.c
Examining data/kma-1.3.7/ef.h
Examining data/kma-1.3.7/filebuff.c
Examining data/kma-1.3.7/filebuff.h
Examining data/kma-1.3.7/frags.c
Examining data/kma-1.3.7/frags.h
Examining data/kma-1.3.7/hashmap.c
Examining data/kma-1.3.7/hashmap.h
Examining data/kma-1.3.7/hashmapcci.c
Examining data/kma-1.3.7/hashmapcci.h
Examining data/kma-1.3.7/hashmapindex.c
Examining data/kma-1.3.7/hashmapindex.h
Examining data/kma-1.3.7/hashmapkma.c
Examining data/kma-1.3.7/hashmapkma.h
Examining data/kma-1.3.7/hashmapkmers.c
Examining data/kma-1.3.7/hashmapkmers.h
Examining data/kma-1.3.7/hashtable.c
Examining data/kma-1.3.7/hashtable.h
Examining data/kma-1.3.7/index.c
Examining data/kma-1.3.7/index.h
Examining data/kma-1.3.7/kma.c
Examining data/kma-1.3.7/kma.h
Examining data/kma-1.3.7/kma_index.c
Examining data/kma-1.3.7/kma_shm.c
Examining data/kma-1.3.7/kma_update.c
Examining data/kma-1.3.7/kmapipe.c
Examining data/kma-1.3.7/kmapipe.h
Examining data/kma-1.3.7/kmathread.h
Examining data/kma-1.3.7/kmeranker.c
Examining data/kma-1.3.7/kmeranker.h
Examining data/kma-1.3.7/kmerlink.c
Examining data/kma-1.3.7/kmerlink.h
Examining data/kma-1.3.7/kmers.c
Examining data/kma-1.3.7/kmers.h
Examining data/kma-1.3.7/kmmap.c
Examining data/kma-1.3.7/kmmap.h
Examining data/kma-1.3.7/loadupdate.c
Examining data/kma-1.3.7/loadupdate.h
Examining data/kma-1.3.7/main.c
Examining data/kma-1.3.7/main.h
Examining data/kma-1.3.7/makeindex.c
Examining data/kma-1.3.7/makeindex.h
Examining data/kma-1.3.7/matrix.c
Examining data/kma-1.3.7/matrix.h
Examining data/kma-1.3.7/mt1.c
Examining data/kma-1.3.7/mt1.h
Examining data/kma-1.3.7/nw.c
Examining data/kma-1.3.7/nw.h
Examining data/kma-1.3.7/penalties.h
Examining data/kma-1.3.7/pherror.c
Examining data/kma-1.3.7/pherror.h
Examining data/kma-1.3.7/printconsensus.c
Examining data/kma-1.3.7/printconsensus.h
Examining data/kma-1.3.7/qseqs.c
Examining data/kma-1.3.7/qseqs.h
Examining data/kma-1.3.7/qualcheck.c
Examining data/kma-1.3.7/qualcheck.h
Examining data/kma-1.3.7/runinput.c
Examining data/kma-1.3.7/runinput.h
Examining data/kma-1.3.7/runkma.c
Examining data/kma-1.3.7/runkma.h
Examining data/kma-1.3.7/sam.c
Examining data/kma-1.3.7/sam.h
Examining data/kma-1.3.7/savekmers.c
Examining data/kma-1.3.7/savekmers.h
Examining data/kma-1.3.7/seq2fasta.c
Examining data/kma-1.3.7/seq2fasta.h
Examining data/kma-1.3.7/seqmenttree.c
Examining data/kma-1.3.7/seqmenttree.h
Examining data/kma-1.3.7/seqparse.c
Examining data/kma-1.3.7/seqparse.h
Examining data/kma-1.3.7/shm.c
Examining data/kma-1.3.7/shm.h
Examining data/kma-1.3.7/sparse.c
Examining data/kma-1.3.7/sparse.h
Examining data/kma-1.3.7/spltdb.c
Examining data/kma-1.3.7/spltdb.h
Examining data/kma-1.3.7/stdnuc.c
Examining data/kma-1.3.7/stdnuc.h
Examining data/kma-1.3.7/stdstat.c
Examining data/kma-1.3.7/stdstat.h
Examining data/kma-1.3.7/threader.h
Examining data/kma-1.3.7/tmp.c
Examining data/kma-1.3.7/tmp.h
Examining data/kma-1.3.7/update.c
Examining data/kma-1.3.7/update.h
Examining data/kma-1.3.7/updateindex.c
Examining data/kma-1.3.7/updateindex.h
Examining data/kma-1.3.7/updatescores.c
Examining data/kma-1.3.7/updatescores.h
Examining data/kma-1.3.7/valueshash.c
Examining data/kma-1.3.7/valueshash.h
Examining data/kma-1.3.7/vcf.c
Examining data/kma-1.3.7/vcf.h
Examining data/kma-1.3.7/version.h
Examining data/kma-1.3.7/xml.c
Examining data/kma-1.3.7/xml.h
FINAL RESULTS:
data/kma-1.3.7/assembly.c:74:10: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "\t%d\t%d\t%d\t%d\t%s\t%s\n", stats[0], stats[1], stats[2], stats[3], template_name, header->seq);
data/kma-1.3.7/db.c:196:5: [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(filename, argv[args]);
data/kma-1.3.7/dist.c:344:16: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
row_bias += sprintf(outfile, "# %-35s\n", method);
data/kma-1.3.7/dist.c:378:18: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
row_bias += sprintf(outfile + row_bias, "\n%s", name);
data/kma-1.3.7/dist.c:475:16: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
row_bias += sprintf(outfile, "# %-35s\n", method);
data/kma-1.3.7/dist.c:509:18: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
row_bias += sprintf(outfile + row_bias, "\n%s", name);
data/kma-1.3.7/dist.c:540:23: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, *++Di));
data/kma-1.3.7/dist.c:544:23: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, D[j][i]));
data/kma-1.3.7/dist.c:549:24: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, *++Di));
data/kma-1.3.7/dist.c:551:24: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, D[j][i]));
data/kma-1.3.7/dist.c:553:24: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
outfile_chunk += sprintf(outfile_chunk, formatString, 100.0);
data/kma-1.3.7/dist.c:894:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(templatefilename, argv[args]);
data/kma-1.3.7/dist.c:984:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outputfilename, "%s.phy", templatefilename);
data/kma-1.3.7/index.c:192:5: [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(outputfilename, argv[args]);
data/kma-1.3.7/index.c:222:5: [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(templatefilename, argv[args]);
data/kma-1.3.7/index.c:473:3: [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(outputfilename, templatefilename);
data/kma-1.3.7/index.c:476:3: [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(outputfilename, *inputfiles);
data/kma-1.3.7/kma.c:83:3: [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(stringPtr, strings[i]);
data/kma-1.3.7/kma.c:276:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(templatefilename, argv[args]);
data/kma-1.3.7/kma.c:286:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(templatefilename, argv[args]);
data/kma-1.3.7/kma.c:426:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(outputfilename, argv[args]);
data/kma-1.3.7/kma.c:992:7: [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(to2Bit, argv[args]);
data/kma-1.3.7/kma.c:1026:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(to2Bit, argv[args]);
data/kma-1.3.7/kma.c:1107:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(myTemplatefilename, templatefilename);
data/kma-1.3.7/kma.c:1154:5: [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(myTemplatefilename, templatefilename);
data/kma-1.3.7/kma.c:1200:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(myTemplatefilename, templatefilename);
data/kma-1.3.7/kma.c:1206:3: [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(myTemplatefilename, templatefilename);
data/kma-1.3.7/kma.c:1211:3: [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(myTemplatefilename, templatefilename);
data/kma-1.3.7/kma.c:1218:3: [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(myTemplatefilename, templatefilename);
data/kma-1.3.7/seq2fasta.c:241:5: [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(filename, argv[args]);
data/kma-1.3.7/shm.c:426:5: [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(templatefilename, argv[args]);
data/kma-1.3.7/tmp.c:48:26: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
tmpname = filename + sprintf(filename, "%s.tmp", location);
data/kma-1.3.7/tmp.c:52:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
tmpname = dirname + sprintf(dirname, "%s.kma-", location);
data/kma-1.3.7/update.c:266:5: [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(filename, argv[args]);
data/kma-1.3.7/vcf.c:57:10: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "##kmaVersion=%s\n", KMA_VERSION);
data/kma-1.3.7/vcf.c:86:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n", noFolder(templateFilename));
data/kma-1.3.7/vcf.c:203:5: [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(update, template_name);
data/kma-1.3.7/vcf.c:240:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "\t%d\t%s\tDP=%d;AD=%d;AF=%.2f;RAF=%.2f;DEL=%d;", QUAL, *FILTER_ptr, DP, AD, AF, RAF, DEL);
data/kma-1.3.7/vcf.c:244:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "Q:P:FT\t%.2f:%4.1e:%s\n", Q, P, FILTER);
data/kma-1.3.7/vcf.c:255:12: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "%s\t%d\t.\t%c\t%c\t%d\t%s\t", template_name, i, nuc, '.', 0, *FILTER_ptr);
data/kma-1.3.7/vcf.c:259:12: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
check = sprintf(update, "Q:P:FT\t%.2f:%4.1e:%s\n", 0.0, 1.0, FILTER);
data/kma-1.3.7/align.c:274:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->t, Frag_align->t + bias, NWstat.len);
data/kma-1.3.7/align.c:275:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->s, Frag_align->s + bias, NWstat.len);
data/kma-1.3.7/align.c:276:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->q, Frag_align->q + bias, NWstat.len);
data/kma-1.3.7/align.c:293:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->t + Stat.len, qseq + q_s, end);
data/kma-1.3.7/align.c:295:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->q + Stat.len, qseq + q_s, end);
data/kma-1.3.7/align.c:352:5: [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(aligned->t + Stat.len, Frag_align->t, NWstat.len);
data/kma-1.3.7/align.c:353:5: [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(aligned->s + Stat.len, Frag_align->s, NWstat.len);
data/kma-1.3.7/align.c:354:5: [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(aligned->q + Stat.len, Frag_align->q, NWstat.len);
data/kma-1.3.7/align.c:408:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->t + Stat.len, Frag_align->t, NWstat.len);
data/kma-1.3.7/align.c:409:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->s + Stat.len, Frag_align->s, NWstat.len);
data/kma-1.3.7/align.c:410:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->q + Stat.len, Frag_align->q, NWstat.len);
data/kma-1.3.7/assembly.c:68:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->next, qseq->seq, qseq->len);
data/kma-1.3.7/assembly.c:88:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:102:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(update, template_name, check);
data/kma-1.3.7/assembly.c:121:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "%c\t%hu\t%hu\t%hu\t%hu\t%hu\t%hu\n", bases[getNuc(template_seq, i)], assembly[pos].counts[0], assembly[pos].counts[1], assembly[pos].counts[2], assembly[pos].counts[3], assembly[pos].counts[4], assembly[pos].counts[5]);
data/kma-1.3.7/assembly.c:124:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "-\t%hu\t%hu\t%hu\t%hu\t%hu\t%hu\n", assembly[pos].counts[0], assembly[pos].counts[1], assembly[pos].counts[2], assembly[pos].counts[3], assembly[pos].counts[4], assembly[pos].counts[5]);
data/kma-1.3.7/assembly.c:207:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:240:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:285:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:783:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:1432:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:1612:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/compress.c:262:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(finalDB->exist, values, finalDB->size * sizeof(unsigned));
data/kma-1.3.7/compress.c:268:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(finalDB->exist_l, values, finalDB->size * sizeof(long unsigned));
data/kma-1.3.7/compress.c:278:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(finalDB->key_index_l, values, (finalDB->n + 1) * sizeof(long unsigned));
data/kma-1.3.7/compress.c:281:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(finalDB->key_index, values, (finalDB->n + 1) * sizeof(unsigned));
data/kma-1.3.7/compress.c:360:5: [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(finalDB->exist, values, finalDB->size * sizeof(unsigned));
data/kma-1.3.7/compress.c:365:5: [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(finalDB->exist_l, values, finalDB->size * sizeof(long unsigned));
data/kma-1.3.7/compress.c:384:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data, finalDB->key_index, (finalDB->n + 1) * sizeof(unsigned));
data/kma-1.3.7/compress.c:389:5: [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(data, finalDB->key_index_l, (finalDB->n + 1) * sizeof(long unsigned));
data/kma-1.3.7/compress.c:396:5: [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(data, finalDB->value_index, finalDB->n * sizeof(unsigned));
data/kma-1.3.7/compress.c:401:5: [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(data, finalDB->value_index_l, finalDB->n * sizeof(long unsigned));
data/kma-1.3.7/compress.c:698:5: [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(finalDB->exist_l, values, finalDB->size * sizeof(unsigned));
data/kma-1.3.7/db.c:31:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/db.c:38:2: [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 Prefix[33];
data/kma-1.3.7/db.c:47:2: [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(filename + filename_len, ".seq.b");
data/kma-1.3.7/db.c:56:2: [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(filename + filename_len, ".comp.b");
data/kma-1.3.7/dist.c:346:15: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
row_bias += sprintf(outfile + row_bias, "%10d", Dist->n);
data/kma-1.3.7/dist.c:380:18: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
row_bias += sprintf(outfile + row_bias, "\n%-10.10s", name);
data/kma-1.3.7/dist.c:401:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
outfile_chunk += sprintf(outfile_chunk, "\t%10d", distPtr(N_i, *++Nj, *++Di));
data/kma-1.3.7/dist.c:477:15: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
row_bias += sprintf(outfile + row_bias, "%10d", Dist->n);
data/kma-1.3.7/dist.c:511:18: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
row_bias += sprintf(outfile + row_bias, "\n%-10.10s", name);
data/kma-1.3.7/dist.c:766:2: [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(templatefilename + file_len, ".comp.b");
data/kma-1.3.7/dist.c:774:2: [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(templatefilename + file_len, ".name");
data/kma-1.3.7/ef.c:32:2: [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 Date[11];
data/kma-1.3.7/frags.c:69:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/frags.c:99:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "\t%d\t%d\t%d", bestHits, best_read_score, *best_start_pos);
data/kma-1.3.7/frags.c:109:11: [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.
check = sprintf(update, ",%d", best_start_pos[i]);
data/kma-1.3.7/frags.c:119:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "\t%d", *best_end_pos);
data/kma-1.3.7/frags.c:128:11: [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.
check = sprintf(update, ",%d", best_end_pos[i]);
data/kma-1.3.7/frags.c:138:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "\t%d", *bestTemplates);
data/kma-1.3.7/frags.c:147:11: [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.
check = sprintf(update, ",%d", bestTemplates[i]);
data/kma-1.3.7/frags.c:160:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(update, header->seq, header->len);
data/kma-1.3.7/hashmapindex.c:397:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".index.b");
data/kma-1.3.7/hashmapindex.c:410:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/index.c:431:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
update = (unsigned char *) argv[args];
data/kma-1.3.7/index.c:622:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".comp.b");
data/kma-1.3.7/index.c:644:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".comp.b");
data/kma-1.3.7/index.c:685:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".decon.comp.b");
data/kma-1.3.7/kma.c:1110:5: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(myTemplatefilename, ".decon.comp.b");
data/kma-1.3.7/kma.c:1112:5: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(myTemplatefilename, ".comp.b");
data/kma-1.3.7/kma.c:1155:5: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(myTemplatefilename, ".length.b");
data/kma-1.3.7/kmapipe.c:40:2: [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 *cmd[2];
data/kma-1.3.7/kmapipe.c:151:2: [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 *argv[2];
data/kma-1.3.7/kmers.c:75:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".decon.comp.b");
data/kma-1.3.7/kmers.c:77:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".comp.b");
data/kma-1.3.7/kmers.c:140:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/loadupdate.c:34:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest, src, size);
data/kma-1.3.7/loadupdate.c:160:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".comp.b");
data/kma-1.3.7/loadupdate.c:172:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/loadupdate.c:197:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/loadupdate.c:198:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".name");
data/kma-1.3.7/loadupdate.c:203:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/loadupdate.c:204:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".seq.b");
data/kma-1.3.7/makeindex.c:63:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".length.b");
data/kma-1.3.7/makeindex.c:67:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".name");
data/kma-1.3.7/makeindex.c:71:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".name");
data/kma-1.3.7/makeindex.c:76:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".seq.b");
data/kma-1.3.7/makeindex.c:80:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".seq.b");
data/kma-1.3.7/mt1.c:120:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".res");
data/kma-1.3.7/mt1.c:124:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag.gz");
data/kma-1.3.7/mt1.c:132:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".aln");
data/kma-1.3.7/mt1.c:135:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/mt1.c:140:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/mt1.c:149:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mat.gz");
data/kma-1.3.7/mt1.c:157:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".vcf.gz");
data/kma-1.3.7/mt1.c:167:5: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".xml");
data/kma-1.3.7/mt1.c:181:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/mt1.c:215:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/mt1.c:222:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/nw.c:62:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->q, query, q_len);
data/kma-1.3.7/nw.c:337:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(aligned->q, query, q_len);
data/kma-1.3.7/pherror.c:39:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *file = fopen(filename, mode);
data/kma-1.3.7/runkma.c:70:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest, src, n);
data/kma-1.3.7/runkma.c:84:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/runkma.c:174:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/runkma.c:193:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/runkma.c:221:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".res");
data/kma-1.3.7/runkma.c:225:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag.gz");
data/kma-1.3.7/runkma.c:233:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".aln");
data/kma-1.3.7/runkma.c:236:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/runkma.c:241:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/runkma.c:254:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mat.gz");
data/kma-1.3.7/runkma.c:261:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag_raw.gz");
data/kma-1.3.7/runkma.c:270:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".vcf.gz");
data/kma-1.3.7/runkma.c:446:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mapstat");
data/kma-1.3.7/runkma.c:469:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".xml");
data/kma-1.3.7/runkma.c:1364:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/runkma.c:1393:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/runkma.c:1422:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".res");
data/kma-1.3.7/runkma.c:1426:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag.gz");
data/kma-1.3.7/runkma.c:1434:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".aln");
data/kma-1.3.7/runkma.c:1437:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/runkma.c:1442:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/runkma.c:1455:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mat.gz");
data/kma-1.3.7/runkma.c:1462:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag_raw.gz");
data/kma-1.3.7/runkma.c:1471:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".vcf.gz");
data/kma-1.3.7/runkma.c:1622:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mapstat");
data/kma-1.3.7/runkma.c:1645:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".xml");
data/kma-1.3.7/sam.c:50:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
cLen = sprintf(cigar, "%dS", aligned->start);
data/kma-1.3.7/sam.c:81:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
cLen += sprintf(cigar + cLen, "%d%c", rep, pop);
data/kma-1.3.7/sam.c:89:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
cLen += sprintf(cigar + cLen, "%d%c", rep, pop);
data/kma-1.3.7/sam.c:92:11: [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.
cLen += sprintf(cigar + cLen, "%dS", aligned->end);
data/kma-1.3.7/sam.c:196:3: [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(cigar, "%dS", *((int*) (header->seq + (header->len - 2 * sizeof(int)))));
data/kma-1.3.7/savekmers.c:4515:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
header->len += sprintf((char *) header->seq + l - 1, "\t%d\t%d", start_cut, end_cut);
data/kma-1.3.7/savekmers.c:4765:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
header->len += sprintf((char *) header->seq + l - 1, "\t%d\t%d", start_cut, end_cut);
data/kma-1.3.7/seq2fasta.c:36:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".length.b");
data/kma-1.3.7/seq2fasta.c:53:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/seq2fasta.c:70:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".seq.b");
data/kma-1.3.7/seq2fasta.c:73:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".name");
data/kma-1.3.7/seq2fasta.c:103:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/seq2fasta.c:128:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".seq.b");
data/kma-1.3.7/seq2fasta.c:131:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".name");
data/kma-1.3.7/seqparse.c:355:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(qual->seq, buff, qual->len);
data/kma-1.3.7/seqparse.c:360:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(seq, buff, avail);
data/kma-1.3.7/seqparse.c:367:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(seq, buff, size);
data/kma-1.3.7/seqparse.c:494:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(qual->seq, buff, qual->len);
data/kma-1.3.7/seqparse.c:499:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(seq, buff, avail);
data/kma-1.3.7/seqparse.c:506:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(seq, buff, size);
data/kma-1.3.7/shm.c:433:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
shmLvl = atoi(argv[args]);
data/kma-1.3.7/shm.c:480:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".comp.b");
data/kma-1.3.7/shm.c:481:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:494:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".decon.comp.b");
data/kma-1.3.7/shm.c:495:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:508:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/shm.c:509:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:523:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/shm.c:524:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:537:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/shm.c:538:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:551:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".comp.b");
data/kma-1.3.7/shm.c:552:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:566:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".decon.comp.b");
data/kma-1.3.7/shm.c:567:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:581:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/shm.c:582:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:601:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/shm.c:602:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/shm.c:620:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/shm.c:621:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(templatefilename, "rb");
data/kma-1.3.7/sparse.c:131:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/sparse.c:163:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/sparse.c:349:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".decon.comp.b");
data/kma-1.3.7/sparse.c:351:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".comp.b");
data/kma-1.3.7/sparse.c:377:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".spa");
data/kma-1.3.7/spltdb.c:132:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, infoSize, (size = sizeof(int) * 8));
data/kma-1.3.7/spltdb.c:134:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, qseq->seq, (size = sizeof(long unsigned) * qseq->complen));
data/kma-1.3.7/spltdb.c:136:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, qseq->N + 1, (size = sizeof(int) * qseq->N[0]));
data/kma-1.3.7/spltdb.c:138:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, out_Tem + 1, (size = sizeof(int) * (*out_Tem)));
data/kma-1.3.7/spltdb.c:140:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, header->seq, header->len);
data/kma-1.3.7/spltdb.c:274:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, infoSize, (size = sizeof(int) * 8));
data/kma-1.3.7/spltdb.c:276:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, qseq->seq, (size = sizeof(long unsigned) * qseq->complen));
data/kma-1.3.7/spltdb.c:278:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, qseq->N + 1, (size = sizeof(int) * qseq->N[0]));
data/kma-1.3.7/spltdb.c:280:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, out_Tem + 1, (size = sizeof(int) * (*out_Tem)));
data/kma-1.3.7/spltdb.c:282:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buff, header->seq, header->len);
data/kma-1.3.7/spltdb.c:416:2: [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 *templatefilename, Date[11];
data/kma-1.3.7/spltdb.c:452:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".length.b");
data/kma-1.3.7/spltdb.c:465:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/spltdb.c:505:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".res");
data/kma-1.3.7/spltdb.c:509:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag.gz");
data/kma-1.3.7/spltdb.c:517:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".aln");
data/kma-1.3.7/spltdb.c:520:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/spltdb.c:525:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".fsa");
data/kma-1.3.7/spltdb.c:538:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mat.gz");
data/kma-1.3.7/spltdb.c:545:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".frag_raw.gz");
data/kma-1.3.7/spltdb.c:554:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".vcf.gz");
data/kma-1.3.7/spltdb.c:561:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".mapstat");
data/kma-1.3.7/spltdb.c:590:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(outputfilename, ".xml");
data/kma-1.3.7/spltdb.c:601:3: [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(outputfilename + file_len, ".%d", i);
data/kma-1.3.7/spltdb.c:602:23: [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).
while(!(inputfile = fopen(outputfilename, "rb"))) {
data/kma-1.3.7/spltdb.c:1538:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/spltdb.c:1548:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/spltdb.c:1569:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".name");
data/kma-1.3.7/spltdb.c:1573:4: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(templatefilename, ".seq.b");
data/kma-1.3.7/stdnuc.c:59:11: [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.
unsigned char carry, comp[6] = {3, 2, 1, 0, 4, 5};
data/kma-1.3.7/stdnuc.c:83:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/tmp.c:53:5: [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(tmpname, "XXXXXX");
data/kma-1.3.7/tmp.c:59:12: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
if((fd = mkstemp(dirname)) == -1) {
data/kma-1.3.7/tmp.c:65:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpname, "XXXXXX");
data/kma-1.3.7/tmp.c:68:3: [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(tmpname, "%d", tmpNum++);
data/kma-1.3.7/tmp.c:69:14: [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((file = fopen(filename, "wb+"))) {
data/kma-1.3.7/tmp.c:75:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
file = tmpfile();
data/kma-1.3.7/update.c:36:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".length.b");
data/kma-1.3.7/update.c:75:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".b");
data/kma-1.3.7/update.c:80:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".comp.b");
data/kma-1.3.7/update.c:151:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".comp.b");
data/kma-1.3.7/update.c:221:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(filename, ".decon.b");
data/kma-1.3.7/update.c:222:9: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(filename, "rb");
data/kma-1.3.7/vcf.c:55:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##fileformat=VCFv4.2\n");
data/kma-1.3.7/vcf.c:61:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##FILTER=<ID=LowQual,Description=\"Low quality\">\n");
data/kma-1.3.7/vcf.c:65:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">\n");
data/kma-1.3.7/vcf.c:67:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=AD,Number=1,Type=Integer,Description=\"Allele Depth\">\n");
data/kma-1.3.7/vcf.c:69:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Fraction\">\n");
data/kma-1.3.7/vcf.c:71:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=RAF,Number=1,Type=Float,Description=\"Revised Allele Fraction\">\n");
data/kma-1.3.7/vcf.c:73:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=DEL,Number=1,Type=Float,Description=\"Fraction of Reads Containing Spanning Deletions\">\n");
data/kma-1.3.7/vcf.c:75:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##INFO=<ID=AD6,Number=6,Type=Integer,Description=\"Count of all alternative alleles: A,C,G,T,N,-\">\n");
data/kma-1.3.7/vcf.c:79:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##FORMAT=<ID=Q,Number=1,Type=Float,Description=\"McNemar quantile\">\n");
data/kma-1.3.7/vcf.c:81:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##FORMAT=<ID=P,Number=1,Type=Float,Description=\"McNemar p-value\">\n");
data/kma-1.3.7/vcf.c:83:10: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "##FORMAT=<ID=FT,Number=1,Type=String,Description=\"Filter\">\n");
data/kma-1.3.7/vcf.c:88:11: [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.
check = sprintf(update, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tspltDB\n");
data/kma-1.3.7/vcf.c:106:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char bases[6] = "ACGTN-";
data/kma-1.3.7/vcf.c:208:14: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "%d", i);
data/kma-1.3.7/vcf.c:242:13: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "AD6=%d,%d,%d,%d,%d,%d\t", assembly[pos].counts[0], assembly[pos].counts[1], assembly[pos].counts[2], assembly[pos].counts[3], assembly[pos].counts[4], assembly[pos].counts[5]);
data/kma-1.3.7/vcf.c:257:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
check = sprintf(update, "DP=%d;AD=%d;AF=%.2f;RAF=%.2f;DEL=%d;AD6=%d,%d,%d,%d,%d,%d\t", 0, 0, 0.0, 0.0, 0, 0, 0, 0, 0, 0, 0);
data/kma-1.3.7/xml.c:153:2: [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 *s, bases[6] = "ACGTN-";
data/kma-1.3.7/assembly.c:54:41: [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).
check = 47 + qseq->len + header->len + strlen(template_name);
data/kma-1.3.7/assembly.c:92:10: [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).
check = strlen(template_name) + 2;
data/kma-1.3.7/assembly.c:352:4: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(100);
data/kma-1.3.7/assembly.c:896:4: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(100);
data/kma-1.3.7/assembly.c:1716:4: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(100);
data/kma-1.3.7/db.c:46:17: [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).
filename_len = strlen(filename);
data/kma-1.3.7/db.c:195:24: [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).
filename = smalloc(strlen(argv[args]) + 64);
data/kma-1.3.7/dist.c:763:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/dist.c:892:17: [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).
file_len = strlen(argv[args]);
data/kma-1.3.7/hashmapcci.c:473:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(size != read(seq, src->seq, size)) {
data/kma-1.3.7/hashmapcci.c:509:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(check != read(seq, src->seq, check)) {
data/kma-1.3.7/hashmapindex.c:292:2: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
data/kma-1.3.7/hashmapindex.c:293:2: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(index, src->index, src->size * sizeof(int));
data/kma-1.3.7/hashmapindex.c:318:2: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
data/kma-1.3.7/hashmapindex.c:399:2: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(index_in, &kmersize, sizeof(int));
data/kma-1.3.7/index.c:191:30: [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).
outputfilename = smalloc(strlen(argv[args]) + 64);
data/kma-1.3.7/index.c:218:31: [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).
templatefilename = malloc(strlen(argv[args]) + 64);
data/kma-1.3.7/index.c:429:19: [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).
prefix_len = strlen(argv[args]);
data/kma-1.3.7/index.c:472:29: [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).
outputfilename = smalloc((strlen(templatefilename) + 64));
data/kma-1.3.7/index.c:475:29: [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).
outputfilename = smalloc((strlen(*inputfiles) + 64));
data/kma-1.3.7/index.c:481:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/kma.c:62:14: [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).
new_len += strlen(strings[i]);
data/kma-1.3.7/kma.c:82:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
new_len = strlen(strings[i]);
data/kma-1.3.7/kma.c:272:32: [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).
templatefilename = malloc(strlen(argv[args]) + 64);
data/kma-1.3.7/kma.c:282:32: [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).
templatefilename = malloc(strlen(argv[args]) + 64);
data/kma-1.3.7/kma.c:422:30: [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).
outputfilename = malloc(strlen(argv[args]) + 64);
data/kma-1.3.7/kma.c:953:18: [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).
size = argc + strlen(outputfilename) + 32;
data/kma-1.3.7/kma.c:960:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += strlen(argv[args]);
data/kma-1.3.7/kma.c:991:17: [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).
exe_len = strlen(argv[args]);
data/kma-1.3.7/kma.c:1025:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
exe_len = strlen(argv[args]);
data/kma-1.3.7/kma.c:1105:14: [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).
exe_len = strlen(templatefilename);
data/kma-1.3.7/kma.c:1153:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
myTemplatefilename = smalloc(strlen(templatefilename) + 64);
data/kma-1.3.7/kma.c:1199:32: [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).
myTemplatefilename = smalloc(strlen(templatefilename) + 64);
data/kma-1.3.7/kma.c:1205:32: [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).
myTemplatefilename = smalloc(strlen(templatefilename) + 64);
data/kma-1.3.7/kma.c:1210:32: [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).
myTemplatefilename = smalloc(strlen(templatefilename) + 64);
data/kma-1.3.7/kma.c:1217:32: [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).
myTemplatefilename = smalloc(strlen(templatefilename) + 64);
data/kma-1.3.7/kmapipe.c:241:4: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(100);
data/kma-1.3.7/kmathread.h:24:5: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
int usleep(unsigned usec);
data/kma-1.3.7/kmathread.h:26:85: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define lock(exclude) while(__sync_lock_test_and_set(exclude, 1)) {while(*exclude) {usleep(100);}}
data/kma-1.3.7/kmathread.h:27:95: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define lockTime(exclude, spin) while(__sync_lock_test_and_set(exclude, 1)) {while(*exclude) {usleep(spin);}}
data/kma-1.3.7/kmathread.h:29:38: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define wait_atomic(src) while(src) {usleep(100);}
data/kma-1.3.7/kmers.c:73:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/loadupdate.c:156:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/loadupdate.c:157:12: [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).
out_len = strlen(outputfilename);
data/kma-1.3.7/makeindex.c:62:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/mt1.c:112:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/mt1.c:180:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/mt1.c:227:25: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(i != Mt1 && (j = fgetc(DB_file)) && j != EOF) {
data/kma-1.3.7/pherror.c:55:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(0 < (nmemb = read(fileno(stream), ptr, size))) {
data/kma-1.3.7/pherror.c:59:5: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(1000);
data/kma-1.3.7/runkma.c:62:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define nameSkip(infile, c) while((c = fgetc(infile)) != '\n' && c != EOF)
data/kma-1.3.7/runkma.c:83:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/runkma.c:122:13: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(infile)) != '\n' && c != EOF) {
data/kma-1.3.7/runkma.c:170:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/runkma.c:210:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/runkma.c:1360:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/runkma.c:1405:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/runkma.h:24:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define nameSkip(infile, c) while((c = fgetc(infile)) != '\n' && c != EOF)
data/kma-1.3.7/seq2fasta.c:35:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/seq2fasta.c:69:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/seq2fasta.c:127:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/seq2fasta.c:239:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(argv[args]);
data/kma-1.3.7/shm.c:421:31: [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).
templatefilename = malloc(strlen(argv[args]) + 64);
data/kma-1.3.7/shm.c:469:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/sparse.c:130:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/sparse.c:347:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/sparse.c:376:14: [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).
file_len = strlen(outputfilename);
data/kma-1.3.7/spltdb.c:451:14: [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).
file_len = strlen(templatefilename);
data/kma-1.3.7/spltdb.c:504:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/spltdb.c:599:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(outputfilename);
data/kma-1.3.7/spltdb.c:603:4: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(100);
data/kma-1.3.7/spltdb.c:1537:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(templatefilename);
data/kma-1.3.7/spltdb.c:1568:15: [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).
file_len = strlen(templatefilename);
data/kma-1.3.7/threader.h:30:85: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define lock(exclude) while(__sync_lock_test_and_set(exclude, 1)) {while(*exclude) {usleep(100);}}
data/kma-1.3.7/threader.h:31:95: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define lockTime(exclude, spin) while(__sync_lock_test_and_set(exclude, 1)) {while(*exclude) {usleep(spin);}}
data/kma-1.3.7/threader.h:33:38: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define wait_atomic(src) while(src) {usleep(100);}
data/kma-1.3.7/tmp.c:46:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(location[strlen(location) - 1] != '/') {
data/kma-1.3.7/tmp.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).
filename = smalloc(strlen(location) + 15);
data/kma-1.3.7/tmp.c:51:23: [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).
dirname = smalloc(strlen(location) + 12);
data/kma-1.3.7/update.c:35:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/update.c:74:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/update.c:213:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
file_len = strlen(filename);
data/kma-1.3.7/update.c:265:24: [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).
filename = smalloc(strlen(argv[args]) + 64);
data/kma-1.3.7/vcf.c:35:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pos = strlen(src) - 1;
data/kma-1.3.7/vcf.c:114:25: [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).
template_name_length = strlen(template_name);
ANALYSIS SUMMARY:
Hits = 351
Lines analyzed = 34449 in approximately 1.33 seconds (25845 lines/second)
Physical Source Lines of Code (SLOC) = 27042
Hits@level = [0] 773 [1] 85 [2] 225 [3] 0 [4] 41 [5] 0
Hits@level+ = [0+] 1124 [1+] 351 [2+] 266 [3+] 41 [4+] 41 [5+] 0
Hits/KSLOC@level+ = [0+] 41.565 [1+] 12.9798 [2+] 9.83655 [3+] 1.51616 [4+] 1.51616 [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.