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/velvet-1.2.10+dfsg1/src/utility.h
Examining data/velvet-1.2.10+dfsg1/src/utility.c
Examining data/velvet-1.2.10+dfsg1/src/tightString.h
Examining data/velvet-1.2.10+dfsg1/src/tightString.c
Examining data/velvet-1.2.10+dfsg1/src/splayTable.h
Examining data/velvet-1.2.10+dfsg1/src/splayTable.c
Examining data/velvet-1.2.10+dfsg1/src/splay.h
Examining data/velvet-1.2.10+dfsg1/src/splay.c
Examining data/velvet-1.2.10+dfsg1/src/shortReadPairs.h
Examining data/velvet-1.2.10+dfsg1/src/shortReadPairs.c
Examining data/velvet-1.2.10+dfsg1/src/scaffold.h
Examining data/velvet-1.2.10+dfsg1/src/scaffold.c
Examining data/velvet-1.2.10+dfsg1/src/run2.c
Examining data/velvet-1.2.10+dfsg1/src/run.h
Examining data/velvet-1.2.10+dfsg1/src/run.c
Examining data/velvet-1.2.10+dfsg1/src/roadMap.h
Examining data/velvet-1.2.10+dfsg1/src/roadMap.c
Examining data/velvet-1.2.10+dfsg1/src/recycleBin.h
Examining data/velvet-1.2.10+dfsg1/src/recycleBin.c
Examining data/velvet-1.2.10+dfsg1/src/readCoherentGraph.h
Examining data/velvet-1.2.10+dfsg1/src/readCoherentGraph.c
Examining data/velvet-1.2.10+dfsg1/src/preGraphConstruction.h
Examining data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c
Examining data/velvet-1.2.10+dfsg1/src/preGraph.h
Examining data/velvet-1.2.10+dfsg1/src/preGraph.c
Examining data/velvet-1.2.10+dfsg1/src/passageMarker.h
Examining data/velvet-1.2.10+dfsg1/src/passageMarker.c
Examining data/velvet-1.2.10+dfsg1/src/locallyCorrectedGraph.h
Examining data/velvet-1.2.10+dfsg1/src/locallyCorrectedGraph.c
Examining data/velvet-1.2.10+dfsg1/src/kseq.h
Examining data/velvet-1.2.10+dfsg1/src/kmerOccurenceTable.h
Examining data/velvet-1.2.10+dfsg1/src/kmer.h
Examining data/velvet-1.2.10+dfsg1/src/kmer.c
Examining data/velvet-1.2.10+dfsg1/src/graphStats.h
Examining data/velvet-1.2.10+dfsg1/src/graphStats.c
Examining data/velvet-1.2.10+dfsg1/src/graphReConstruction.h
Examining data/velvet-1.2.10+dfsg1/src/graphReConstruction.c
Examining data/velvet-1.2.10+dfsg1/src/graph.h
Examining data/velvet-1.2.10+dfsg1/src/graph.c
Examining data/velvet-1.2.10+dfsg1/src/globals.h
Examining data/velvet-1.2.10+dfsg1/src/fibpriv.h
Examining data/velvet-1.2.10+dfsg1/src/fibHeap.h
Examining data/velvet-1.2.10+dfsg1/src/fibHeap.c
Examining data/velvet-1.2.10+dfsg1/src/fib.h
Examining data/velvet-1.2.10+dfsg1/src/fib.c
Examining data/velvet-1.2.10+dfsg1/src/dfibpriv.h
Examining data/velvet-1.2.10+dfsg1/src/dfibHeap.h
Examining data/velvet-1.2.10+dfsg1/src/dfibHeap.c
Examining data/velvet-1.2.10+dfsg1/src/dfib.h
Examining data/velvet-1.2.10+dfsg1/src/dfib.c
Examining data/velvet-1.2.10+dfsg1/src/correctedGraph.h
Examining data/velvet-1.2.10+dfsg1/src/concatenatedPreGraph.h
Examining data/velvet-1.2.10+dfsg1/src/concatenatedPreGraph.c
Examining data/velvet-1.2.10+dfsg1/src/concatenatedGraph.h
Examining data/velvet-1.2.10+dfsg1/src/concatenatedGraph.c
Examining data/velvet-1.2.10+dfsg1/src/binarySequences.h
Examining data/velvet-1.2.10+dfsg1/src/autoOpen.h
Examining data/velvet-1.2.10+dfsg1/src/autoOpen.c
Examining data/velvet-1.2.10+dfsg1/src/allocArray.h
Examining data/velvet-1.2.10+dfsg1/src/allocArray.c
Examining data/velvet-1.2.10+dfsg1/src/binarySequences.c
Examining data/velvet-1.2.10+dfsg1/src/readSet.c
Examining data/velvet-1.2.10+dfsg1/src/readSet.h
Examining data/velvet-1.2.10+dfsg1/src/correctedGraph.c
Examining data/velvet-1.2.10+dfsg1/src/kmerOccurenceTable.c
Examining data/velvet-1.2.10+dfsg1/contrib/solaris/recycleBin.c
Examining data/velvet-1.2.10+dfsg1/contrib/shuffleSequences_fasta/shuffleSeqs-fast.c
Examining data/velvet-1.2.10+dfsg1/contrib/shuffleSequences_fasta/kseq.h
FINAL RESULTS:
data/velvet-1.2.10+dfsg1/src/autoOpen.c:33:3: [4] (shell) execvp:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
execvp(exe, (char**)argv);
data/velvet-1.2.10+dfsg1/src/binarySequences.c:471:5: [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(seqNamesFileName, unifiedSeqFileName);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1089:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(logFilename, directory);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1848:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(logFilename, directory);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1881:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(outFilename, directory);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1977:5: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
sscanf(strtok(line, ":-\r\n"), ">%s", name);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1984:6: [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(refCoords[refIndex].name, name);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1989:6: [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(refCoords[refIndex].name, name);
data/velvet-1.2.10+dfsg1/src/graphStats.c:2000:5: [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(name, line + 1);
data/velvet-1.2.10+dfsg1/src/graphStats.c:2002:5: [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(refCoords[refIndex].name, name);
data/velvet-1.2.10+dfsg1/src/passageMarker.c:288:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s, "%s START -> %ld", s,
data/velvet-1.2.10+dfsg1/src/passageMarker.c:291:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s, "%s %ld -> %ld", s,
data/velvet-1.2.10+dfsg1/src/passageMarker.c:296:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s, "%s -> FINISH", s);
data/velvet-1.2.10+dfsg1/src/passageMarker.c:298:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s, "%s -> %ld ", s,
data/velvet-1.2.10+dfsg1/src/readSet.c:366:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(name, ">%s", seq_name);
data/velvet-1.2.10+dfsg1/src/readSet.c:521:5: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
sscanf(strtok(line, ":-\r\n\t "), ">%s", name);
data/velvet-1.2.10+dfsg1/src/readSet.c:534:5: [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(name, line + 1);
data/velvet-1.2.10+dfsg1/src/readSet.c:771:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(print_qname, ">%s%s", previous_qname, previous_qname_pairing);
data/velvet-1.2.10+dfsg1/src/readSet.c:921:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(previous_qname, qname);
data/velvet-1.2.10+dfsg1/src/readSet.c:922:5: [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(previous_qname_pairing, qname_pairing);
data/velvet-1.2.10+dfsg1/src/readSet.c:923:5: [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(previous_seq, seq);
data/velvet-1.2.10+dfsg1/src/readSet.c:1029:3: [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(refNames[i], (char *) buffer);
data/velvet-1.2.10+dfsg1/src/readSet.c:1080:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cigar, cigar_buffer);
data/velvet-1.2.10+dfsg1/src/readSet.c:1118:4: [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(previous_qname, qname);
data/velvet-1.2.10+dfsg1/src/readSet.c:1119:4: [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(previous_qname_pairing, qname_pairing);
data/velvet-1.2.10+dfsg1/src/readSet.c:1120:4: [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(previous_seq, seq);
data/velvet-1.2.10+dfsg1/src/readSet.c:1639:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(logFilename, directory);
data/velvet-1.2.10+dfsg1/src/run.c:141:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(buffer, argv[2]);
data/velvet-1.2.10+dfsg1/src/run.c:215:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"%s_%d",argv[1],h);
data/velvet-1.2.10+dfsg1/src/run.c:217:4: [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(directory,buf);
data/velvet-1.2.10+dfsg1/src/run.c:230:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/PreGraph", directory);
data/velvet-1.2.10+dfsg1/src/run.c:232:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/Graph", directory);
data/velvet-1.2.10+dfsg1/src/run.c:234:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/Graph2", directory);
data/velvet-1.2.10+dfsg1/src/run.c:236:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/Graph3", directory);
data/velvet-1.2.10+dfsg1/src/run.c:238:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/Graph4", directory);
data/velvet-1.2.10+dfsg1/src/run.c:244:3: [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(seqFilename, directory);
data/velvet-1.2.10+dfsg1/src/run.c:249:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/Sequences", directory);
data/velvet-1.2.10+dfsg1/src/run.c:254:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/CnyUnifiedSeq", directory);
data/velvet-1.2.10+dfsg1/src/run.c:256:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf, "%s/CnyUnifiedSeq.names", directory);
data/velvet-1.2.10+dfsg1/src/run.c:259:3: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(seqFilename, baseSeqName);
data/velvet-1.2.10+dfsg1/src/run.c:264:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"rm -f %s",seqFilename);
data/velvet-1.2.10+dfsg1/src/run.c:265:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system(buf)) {
data/velvet-1.2.10+dfsg1/src/run.c:274:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"ln -s %s_%d%s %s",argv[1],hashLength,baseSeqName,seqFilename);
data/velvet-1.2.10+dfsg1/src/run.c:276:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"ln -s `pwd`/%s_%d%s %s",argv[1],hashLength,baseSeqName,seqFilename);
data/velvet-1.2.10+dfsg1/src/run.c:277:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system(buf)) {
data/velvet-1.2.10+dfsg1/src/run.c:298:3: [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(filename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:370:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:373:6: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access(seqFilename, R_OK) == 0) {
data/velvet-1.2.10+dfsg1/src/run2.c:377:3: [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(seqFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:381:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(roadmapFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:384:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(preGraphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:387:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(connectedGraphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:391:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:394:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:398:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(lowCovContigsFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:401:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(highCovContigsFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:420:4: [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(compareSeqFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:485:4: [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(compareSeqFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:635:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:641:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:647:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:652:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:658:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:674:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:678:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:684:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:688:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/run2.c:692:3: [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(graphFilename, directory);
data/velvet-1.2.10+dfsg1/src/splayTable.c:989:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(seqReadInfo.m_namesFilename, "%s.names", seqFilename);
data/velvet-1.2.10+dfsg1/src/utility.c:86:8: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, args);
data/velvet-1.2.10+dfsg1/src/utility.c:117:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(format, args);
data/velvet-1.2.10+dfsg1/src/utility.c:130:6: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
if (vfprintf(file, format, args) < 0) {
data/velvet-1.2.10+dfsg1/src/utility.c:189:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
buffer->str = strcat(buffer->str, str);
data/velvet-1.2.10+dfsg1/src/utility.h:66:26: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
ATTRIBUTE((format(printf, 3, 4), noreturn));
data/velvet-1.2.10+dfsg1/src/utility.h:70:20: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
ATTRIBUTE((format(printf, 1, 2)));
data/velvet-1.2.10+dfsg1/src/utility.h:74:20: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
ATTRIBUTE((format(printf, 2, 3)));
data/velvet-1.2.10+dfsg1/contrib/shuffleSequences_fasta/kseq.h:123:4: [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(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/velvet-1.2.10+dfsg1/src/autoOpen.c:68:20: [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).
seqFile->file = fopen(filename, "r");
data/velvet-1.2.10+dfsg1/src/binarySequences.c:59:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pFile = fopen(fileName, "rb")) == 0) {
data/velvet-1.2.10+dfsg1/src/binarySequences.c:469:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seqNamesFileName[5000];
data/velvet-1.2.10+dfsg1/src/binarySequences.c:472:5: [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(seqNamesFileName, ".names");
data/velvet-1.2.10+dfsg1/src/binarySequences.c:480:34: [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 ((seqWriteInfo->m_pFile = fopen(unifiedSeqFileName, "wb")) == 0) {
data/velvet-1.2.10+dfsg1/src/binarySequences.c:485:37: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((seqWriteInfo->m_nameFile = fopen(seqNamesFileName, "w")) == 0) {
data/velvet-1.2.10+dfsg1/src/binarySequences.c:490:5: [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(&seqWriteInfo->m_unifiedSeqFileHeader.m_magic, "CSQ0", 4);
data/velvet-1.2.10+dfsg1/src/graph.c:1961:12: [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).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graph.c:2030:15: [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, "r");
data/velvet-1.2.10+dfsg1/src/graph.c:2032:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graph.c:2265:15: [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(preGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graph.c:2267:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graph.c:2423:15: [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(connectedGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graph.c:2425:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:264:15: [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(preGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:266:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:285:15: [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(preGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:287:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:469:15: [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(preGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:471:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:526:9: [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(preGraphFilename, "r");
data/velvet-1.2.10+dfsg1/src/graphStats.c:462:12: [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).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:704:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:968:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1090:2: [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(logFilename, "/Log");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1091:12: [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).
logFile = fopen(logFilename, "a");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1241:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1347:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile = fopen(filename, "a");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1409:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1557:2: [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 str[100];
data/velvet-1.2.10+dfsg1/src/graphStats.c:1674:2: [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 str[100];
data/velvet-1.2.10+dfsg1/src/graphStats.c:1714:12: [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).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1849:2: [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(logFilename, "/Log");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1850:12: [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).
logFile = fopen(logFilename, "a");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1856:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf
data/velvet-1.2.10+dfsg1/src/graphStats.c:1882:2: [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(outFilename, "/UnusedReads.fa");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1883:12: [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).
outfile = fopen(outFilename, "w");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1961:3: [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(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1967:20: [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(seqReadInfo->m_seqFilename, "r");
data/velvet-1.2.10+dfsg1/src/graphStats.c:1968:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/graphStats.c:1969:2: [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 name[5000];
data/velvet-1.2.10+dfsg1/src/graphStats.c:2125:12: [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).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/kseq.h:123:4: [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(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/velvet-1.2.10+dfsg1/src/passageMarker.c:284:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "MARKER %ld (%lld -> %lld):", (long) markerVal->sequenceID,
data/velvet-1.2.10+dfsg1/src/preGraph.c:1205:12: [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).
outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:399:2: [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 line[50000];
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:410:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(sequenceFilename, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:363:2: [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 name[5001];
data/velvet-1.2.10+dfsg1/src/readSet.c:375:2: [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 str[100];
data/velvet-1.2.10+dfsg1/src/readSet.c:421:2: [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 line[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:427:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(filename, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:461:2: [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 line[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:500:2: [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 line[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:509:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file = fopen(filename, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:763:2: [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 print_qname[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:817:2: [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 line[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:820:2: [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 previous_qname_pairing[10];
data/velvet-1.2.10+dfsg1/src/readSet.c:821:2: [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 previous_qname[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:822:2: [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 previous_seq[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:844:45: [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 = (strcmp(filename, "-") != 0)? fopen(filename, "r") : stdin;
data/velvet-1.2.10+dfsg1/src/readSet.c:947:11: [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 buffer[4];
data/velvet-1.2.10+dfsg1/src/readSet.c:958:2: [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 cigar[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:959:2: [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 cigar_buffer[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:965:2: [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 previous_qname_pairing[10];
data/velvet-1.2.10+dfsg1/src/readSet.c:966:2: [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 previous_qname[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:967:2: [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 previous_seq[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:1079:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cigar_buffer, "%i%c", packed >> 4, decode_ops[packed & 0xf]);
data/velvet-1.2.10+dfsg1/src/readSet.c:1227:27: [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).
seqWriteInfo->m_pFile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/readSet.c:1526:15: [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, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:1530:2: [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 line[5000];
data/velvet-1.2.10+dfsg1/src/readSet.c:1562:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:1597:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/readSet.c:1640:2: [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(logFilename, "/Log");
data/velvet-1.2.10+dfsg1/src/readSet.c:1641:12: [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).
logFile = fopen(logFilename, "a");
data/velvet-1.2.10+dfsg1/src/roadMap.c:115:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/roadMap.c:145:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/roadMap.c:212:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/roadMap.c:248:9: [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, "r");
data/velvet-1.2.10+dfsg1/src/run.c:106:2: [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 buffer[100];
data/velvet-1.2.10+dfsg1/src/run.c:143:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
hashLength = atoi(token);
data/velvet-1.2.10+dfsg1/src/run.c:150:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
hashLengthMax = atoi(token);
data/velvet-1.2.10+dfsg1/src/run.c:156:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
hashLengthStep = atoi(token);
data/velvet-1.2.10+dfsg1/src/run.c:247:4: [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(baseSeqName, "/CnyUnifiedSeq");
data/velvet-1.2.10+dfsg1/src/run.c:252:4: [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(baseSeqName, "/Sequences");
data/velvet-1.2.10+dfsg1/src/run.c:299:3: [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(filename, "/Roadmaps");
data/velvet-1.2.10+dfsg1/src/run2.c:372:2: [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(seqFilename, "/CnyUnifiedSeq");
data/velvet-1.2.10+dfsg1/src/run2.c:378:2: [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(seqFilename, "/Sequences");
data/velvet-1.2.10+dfsg1/src/run2.c:382:2: [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(roadmapFilename, "/Roadmaps");
data/velvet-1.2.10+dfsg1/src/run2.c:385:2: [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(preGraphFilename, "/PreGraph");
data/velvet-1.2.10+dfsg1/src/run2.c:388:2: [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(connectedGraphFilename, "/ConnectedGraph");
data/velvet-1.2.10+dfsg1/src/run2.c:392:3: [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(graphFilename, "/Graph");
data/velvet-1.2.10+dfsg1/src/run2.c:395:3: [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(graphFilename, "/Graph2");
data/velvet-1.2.10+dfsg1/src/run2.c:399:2: [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(lowCovContigsFilename, "/lowCoverageContigs.fa");
data/velvet-1.2.10+dfsg1/src/run2.c:402:2: [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(highCovContigsFilename, "/highCoverageContigs.fa");
data/velvet-1.2.10+dfsg1/src/run2.c:405:14: [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(graphFilename, "r")) != NULL) {
data/velvet-1.2.10+dfsg1/src/run2.c:410:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((file = fopen(connectedGraphFilename, "r")) != NULL) {
data/velvet-1.2.10+dfsg1/src/run2.c:421:4: [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(compareSeqFilename, "/Sequences");
data/velvet-1.2.10+dfsg1/src/run2.c:457:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((file = fopen(preGraphFilename, "r")) != NULL) {
data/velvet-1.2.10+dfsg1/src/run2.c:473:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
} else if ((file = fopen(roadmapFilename, "r")) != NULL) {
data/velvet-1.2.10+dfsg1/src/run2.c:486:4: [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(compareSeqFilename, "/Sequences");
data/velvet-1.2.10+dfsg1/src/run2.c:636:2: [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(graphFilename, "/contigs.fa");
data/velvet-1.2.10+dfsg1/src/run2.c:642:3: [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(graphFilename, "/contig-alignments.psa");
data/velvet-1.2.10+dfsg1/src/run2.c:648:2: [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(graphFilename, "/stats.txt");
data/velvet-1.2.10+dfsg1/src/run2.c:653:3: [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(graphFilename, "/LastGraph");
data/velvet-1.2.10+dfsg1/src/run2.c:659:3: [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(graphFilename, "/velvet_asm.afg");
data/velvet-1.2.10+dfsg1/src/run2.c:675:3: [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(graphFilename, "/Roadmaps");
data/velvet-1.2.10+dfsg1/src/run2.c:679:3: [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(graphFilename, "/LastGraph");
data/velvet-1.2.10+dfsg1/src/run2.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(graphFilename, "/Sequences");
data/velvet-1.2.10+dfsg1/src/run2.c:689:3: [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(graphFilename, "/Graph2");
data/velvet-1.2.10+dfsg1/src/run2.c:693:3: [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(graphFilename, "/Graph");
data/velvet-1.2.10+dfsg1/src/splayTable.c:429:2: [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 lineBuffer[MAXLINE];
data/velvet-1.2.10+dfsg1/src/splayTable.c:443:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(lineBuffer, "ROADMAP %li\n", (long)seqID);
data/velvet-1.2.10+dfsg1/src/splayTable.c:540:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
data/velvet-1.2.10+dfsg1/src/splayTable.c:576:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
data/velvet-1.2.10+dfsg1/src/splayTable.c:596:3: [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(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
data/velvet-1.2.10+dfsg1/src/splayTable.c:768:2: [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 lineBuffer[MAXLINE];
data/velvet-1.2.10+dfsg1/src/splayTable.c:776:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(lineBuffer, "ROADMAP %li\n", (long)currentIndex);
data/velvet-1.2.10+dfsg1/src/splayTable.c:867:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/splayTable.c:912:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/splayTable.c:914:15: [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(seqReadInfo->m_namesFilename, "r");
data/velvet-1.2.10+dfsg1/src/splayTable.c:975:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *outfile = fopen(filename, "w");
data/velvet-1.2.10+dfsg1/src/splayTable.c:1005:2: [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 line[MAXLINE];
data/velvet-1.2.10+dfsg1/src/splayTable.c:1089:14: [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).
seqFile = fopen(seqFilename, "r");
data/velvet-1.2.10+dfsg1/src/tightString.c:189:3: [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(string, "VOID");
data/velvet-1.2.10+dfsg1/src/tightString.c:345:2: [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 str[100];
data/velvet-1.2.10+dfsg1/src/autoOpen.c:67:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(decompressors[i])==0) {
data/velvet-1.2.10+dfsg1/src/autoOpen.c:81:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int c = fgetc(seqFile->file);
data/velvet-1.2.10+dfsg1/src/graph.c:2115:15: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(file)) != '\n' && c != EOF) {
data/velvet-1.2.10+dfsg1/src/graph.c:2143:15: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(file)) != '\n' && c != EOF) {
data/velvet-1.2.10+dfsg1/src/graph.c:2329:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(file)) != '\n') {
data/velvet-1.2.10+dfsg1/src/graph.c:2512:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(file)) != '\n') {
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:504:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(file)) != EOF && c != '\n')
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:544:8: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(file);
data/velvet-1.2.10+dfsg1/src/graphReConstruction.c:571:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = getc(file)) != '\n' && c != EOF) {
data/velvet-1.2.10+dfsg1/src/graphStats.c:1084:19: [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).
mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1572:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(str, &(string[start]), 60);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1580:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(str, &(string[start]), 60);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1843:19: [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).
mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1872:19: [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).
mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1982:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);
data/velvet-1.2.10+dfsg1/src/graphStats.c:1995:14: [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).
for (i = strlen(line) - 1;
data/velvet-1.2.10+dfsg1/src/graphStats.c:2001:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);
data/velvet-1.2.10+dfsg1/src/preGraph.c:1024:13: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
letter = getc(seqReadInfo->m_pFile);
data/velvet-1.2.10+dfsg1/src/preGraph.c:1026:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
letter = getc(seqReadInfo->m_pFile);
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:460:8: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(file);
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:462:9: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(file);
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:564:10: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(file);
data/velvet-1.2.10+dfsg1/src/preGraphConstruction.c:566:11: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(file);
data/velvet-1.2.10+dfsg1/src/readSet.c:240:18: [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_t length = strlen(str);
data/velvet-1.2.10+dfsg1/src/readSet.c:293:18: [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_t length = strlen(str);
data/velvet-1.2.10+dfsg1/src/readSet.c:328:18: [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_t length = strlen(str);
data/velvet-1.2.10+dfsg1/src/readSet.c:354:18: [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_t length = strlen(line);
data/velvet-1.2.10+dfsg1/src/readSet.c:358:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(file);
data/velvet-1.2.10+dfsg1/src/readSet.c:382:19: [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).
while (start <= strlen(seq)) {
data/velvet-1.2.10+dfsg1/src/readSet.c:383:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(str, seq + start, 60);
data/velvet-1.2.10+dfsg1/src/readSet.c:437:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(line) >= maxline - 1) {
data/velvet-1.2.10+dfsg1/src/readSet.c:478:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(line) >= maxline - 1) {
data/velvet-1.2.10+dfsg1/src/readSet.c:518:24: [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).
name = callocOrExit(strlen(line), char);
data/velvet-1.2.10+dfsg1/src/readSet.c:530:12: [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).
for (i=strlen(line) - 1; i >= 0; i--)
data/velvet-1.2.10+dfsg1/src/readSet.c:736:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refElem->m_elem.m_pos = (long long) (refCoord->finish - pos - strlen(seq));
data/velvet-1.2.10+dfsg1/src/readSet.c:750:147: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq)));
data/velvet-1.2.10+dfsg1/src/readSet.c:752:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (*buffer_size - strlen(buffer) < 100) {
data/velvet-1.2.10+dfsg1/src/readSet.c:779:3: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(buffer, "");
data/velvet-1.2.10+dfsg1/src/readSet.c:788:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(cigar) == 1 && cigar[0] == '*')
data/velvet-1.2.10+dfsg1/src/readSet.c:792:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (cigar_index = 0; cigar_index < strlen(cigar); cigar_index++) {
data/velvet-1.2.10+dfsg1/src/readSet.c:852:2: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(previous_qname, "");
data/velvet-1.2.10+dfsg1/src/readSet.c:890:9: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(rname, "");
data/velvet-1.2.10+dfsg1/src/readSet.c:917:121: [1] (buffer) strlen:
Does not handle 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 (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, rname, (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation))) {
data/velvet-1.2.10+dfsg1/src/readSet.c:1034:2: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(previous_qname, "");
data/velvet-1.2.10+dfsg1/src/readSet.c:1075:4: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(cigar, "");
data/velvet-1.2.10+dfsg1/src/readSet.c:1115:128: [1] (buffer) strlen:
Does not handle 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 (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, refNames[rID], (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation)))
data/velvet-1.2.10+dfsg1/src/readSet.c:1231:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (argv[argIndex][0] == '-' && strlen(argv[argIndex]) > 1) {
data/velvet-1.2.10+dfsg1/src/readSet.c:1580:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
bpCount += (Coordinate) strlen(line) - 1;
data/velvet-1.2.10+dfsg1/src/readSet.c:1612:17: [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).
lineLength = strlen(line) - 1;
data/velvet-1.2.10+dfsg1/src/readSet.c:1613:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(sequence + bpCount, line, lineLength);
data/velvet-1.2.10+dfsg1/src/readSet.c:1631:19: [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).
mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run.c:212:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
buf = mallocOrExit(2 * strlen(argv[1]) + 500, char);
data/velvet-1.2.10+dfsg1/src/run.c:216:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
directory = mallocOrExit(strlen(buf) + 100, char);
data/velvet-1.2.10+dfsg1/src/run.c:221:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
filename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run.c:222:30: [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).
seqFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:169:31: [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).
graphFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:170:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
connectedGraphFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:172:19: [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).
mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:173:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
roadmapFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:174:29: [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).
seqFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:175:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
lowCovContigsFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:176:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
highCovContigsFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:419:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
compareSeqFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/run2.c:484:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char *compareSeqFilename = mallocOrExit(strlen(directory) + 100, char);
data/velvet-1.2.10+dfsg1/src/splayTable.c:880:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(file))) {
data/velvet-1.2.10+dfsg1/src/splayTable.c:930:12: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c = getc(file)) != '>') {
data/velvet-1.2.10+dfsg1/src/splayTable.c:944:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(file))) {
data/velvet-1.2.10+dfsg1/src/splayTable.c:988:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seqReadInfo.m_namesFilename = mallocOrExit(strlen(seqFilename) + sizeof(".names"), char);
data/velvet-1.2.10+dfsg1/src/splayTable.c:1201:27: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (seqFile && (c = getc(seqFile)) != EOF) {
data/velvet-1.2.10+dfsg1/src/tightString.c:146:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tStringArray[sequenceIndex].length = strlen (sequences[sequenceIndex]);
data/velvet-1.2.10+dfsg1/src/utility.c:176:12: [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).
strSize = strlen(str);
ANALYSIS SUMMARY:
Hits = 273
Lines analyzed = 30260 in approximately 0.62 seconds (48886 lines/second)
Physical Source Lines of Code (SLOC) = 23114
Hits@level = [0] 125 [1] 71 [2] 126 [3] 0 [4] 76 [5] 0
Hits@level+ = [0+] 398 [1+] 273 [2+] 202 [3+] 76 [4+] 76 [5+] 0
Hits/KSLOC@level+ = [0+] 17.219 [1+] 11.811 [2+] 8.73929 [3+] 3.28805 [4+] 3.28805 [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.