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/snap-2013-11-29/fathom.c
Examining data/snap-2013-11-29/forge.c
Examining data/snap-2013-11-29/hmm-info.c
Examining data/snap-2013-11-29/Zoe/lexica.c
Examining data/snap-2013-11-29/Zoe/seqedit.c
Examining data/snap-2013-11-29/Zoe/seqstats.c
Examining data/snap-2013-11-29/Zoe/twinkle.c
Examining data/snap-2013-11-29/Zoe/zoe-loop.c
Examining data/snap-2013-11-29/Zoe/zoe.h
Examining data/snap-2013-11-29/Zoe/zoeAlignment.h
Examining data/snap-2013-11-29/Zoe/zoeCDS.c
Examining data/snap-2013-11-29/Zoe/zoeCDS.h
Examining data/snap-2013-11-29/Zoe/zoeCounter.c
Examining data/snap-2013-11-29/Zoe/zoeCounter.h
Examining data/snap-2013-11-29/Zoe/zoeDistribution.c
Examining data/snap-2013-11-29/Zoe/zoeDistribution.h
Examining data/snap-2013-11-29/Zoe/zoeDNA.c
Examining data/snap-2013-11-29/Zoe/zoeDNA.h
Examining data/snap-2013-11-29/Zoe/zoeDuration.c
Examining data/snap-2013-11-29/Zoe/zoeDuration.h
Examining data/snap-2013-11-29/Zoe/zoeFastaFile.c
Examining data/snap-2013-11-29/Zoe/zoeFastaFile.h
Examining data/snap-2013-11-29/Zoe/zoeFeature.c
Examining data/snap-2013-11-29/Zoe/zoeFeature.h
Examining data/snap-2013-11-29/Zoe/zoeFeatureFactory.c
Examining data/snap-2013-11-29/Zoe/zoeFeatureFactory.h
Examining data/snap-2013-11-29/Zoe/zoeFeatureTable.c
Examining data/snap-2013-11-29/Zoe/zoeFeatureTable.h
Examining data/snap-2013-11-29/Zoe/zoeHMM.c
Examining data/snap-2013-11-29/Zoe/zoeHMM.h
Examining data/snap-2013-11-29/Zoe/zoeIsochore.c
Examining data/snap-2013-11-29/Zoe/zoeIsochore.h
Examining data/snap-2013-11-29/Zoe/zoeMath.c
Examining data/snap-2013-11-29/Zoe/zoeMath.h
Examining data/snap-2013-11-29/Zoe/zoeModel.c
Examining data/snap-2013-11-29/Zoe/zoeModel.h
Examining data/snap-2013-11-29/Zoe/zoePhasePref.h
Examining data/snap-2013-11-29/Zoe/zoeProtein.c
Examining data/snap-2013-11-29/Zoe/zoeProtein.h
Examining data/snap-2013-11-29/Zoe/zoeScanner.c
Examining data/snap-2013-11-29/Zoe/zoeScanner.h
Examining data/snap-2013-11-29/Zoe/zoeState.c
Examining data/snap-2013-11-29/Zoe/zoeState.h
Examining data/snap-2013-11-29/Zoe/zoeTransition.c
Examining data/snap-2013-11-29/Zoe/zoeTransition.h
Examining data/snap-2013-11-29/Zoe/zoeTrellis.c
Examining data/snap-2013-11-29/Zoe/zoeTrellis.h
Examining data/snap-2013-11-29/Zoe/zoeAlignment.c
Examining data/snap-2013-11-29/Zoe/zoeTools.c
Examining data/snap-2013-11-29/Zoe/zoePhasePref.c
Examining data/snap-2013-11-29/Zoe/zoeTools.h
Examining data/snap-2013-11-29/exonpairs.c
Examining data/snap-2013-11-29/snap.c

FINAL RESULTS:

data/snap-2013-11-29/Zoe/zoeCDS.c:411:47:  [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).
	cds->name     = zoeMalloc(strlen(name) + 1); strcpy(cds->name, name);
data/snap-2013-11-29/Zoe/zoeDNA.c:124:2:  [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(dna->def, def);
data/snap-2013-11-29/Zoe/zoeDNA.c:125:2:  [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(dna->seq, seq);
data/snap-2013-11-29/Zoe/zoeDistribution.c:73:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %d %d", func_name, &start, &end) != 3) {
data/snap-2013-11-29/Zoe/zoeDistribution.c:99:8:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	 	if (fscanf(stream, "%s", input) != 1) {
data/snap-2013-11-29/Zoe/zoeDuration.c:80:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %d", duration_name, &distributions) != 2) {
data/snap-2013-11-29/Zoe/zoeFastaFile.c:56:2:  [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(ff->def, def);
data/snap-2013-11-29/Zoe/zoeFastaFile.c:57:2:  [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(ff->seq, seq);
data/snap-2013-11-29/Zoe/zoeFeature.c:74:3:  [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(f->group, group);
data/snap-2013-11-29/Zoe/zoeFeature.c:113:6:  [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.
	if (sscanf(line, "%s %s %s %s %s %s %s %s %s", /* group */
data/snap-2013-11-29/Zoe/zoeFeature.c:117:13:  [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.
	} else if (sscanf(line, "%s %s %s %s %s %s %s %s", /* no group */
data/snap-2013-11-29/Zoe/zoeFeature.c:121:13:  [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.
	} else if (sscanf(line, "%s %s %s %s", /* short form w/ group */
data/snap-2013-11-29/Zoe/zoeFeature.c:125:13:  [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.
	} else if (sscanf(line, "%s %s %s", /* short form w/o group */
data/snap-2013-11-29/Zoe/zoeFeature.c:186:6:  [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.
	if (sscanf(line, "%s %s %s %s %s %s %s %s %s", /* group */
data/snap-2013-11-29/Zoe/zoeFeature.c:189:13:  [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.
	} else if (sscanf(line, "%s %s %s %s %s %s %s %s", /* no group */
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:116:8:  [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).
	(void)strcpy(ft->def, def);
data/snap-2013-11-29/Zoe/zoeHMM.c:58:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s", tmp) != 1) {
data/snap-2013-11-29/Zoe/zoeHMM.c:399:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %s %d %d %d %d", type, name, &states,
data/snap-2013-11-29/Zoe/zoeHMM.c:409:27:  [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).
	                   (void)strcpy(hmm->name, name);
data/snap-2013-11-29/Zoe/zoeHMM.c:500:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(path, "%s/HMM/%s", ZOE, file);
data/snap-2013-11-29/Zoe/zoeIsochore.c:81:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %d", name, &count) != 2)
data/snap-2013-11-29/Zoe/zoeIsochore.c:88:7:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
		if (fscanf(stream, "%f %f %s", &min, &max, name) != 3) zoeExit("zoeReadIsochore format error");
data/snap-2013-11-29/Zoe/zoeIsochore.c:107:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(path, "%s/HMM/%s", ZOE, file);
data/snap-2013-11-29/Zoe/zoeModel.c:47:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %s %d %d %d %d %f",
data/snap-2013-11-29/Zoe/zoeModel.c:61:8:  [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).
	(void)strcpy(model->name, name);
data/snap-2013-11-29/Zoe/zoeModel.c:86:9:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
				if (fscanf(stream, "%s", data) != 1) {
data/snap-2013-11-29/Zoe/zoeModel.c:103:9:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
				if (fscanf(stream, "%s", data) != 1) {
data/snap-2013-11-29/Zoe/zoeProtein.c:117:2:  [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(pro->def, def);
data/snap-2013-11-29/Zoe/zoeProtein.c:118:2:  [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(pro->seq, seq);
data/snap-2013-11-29/Zoe/zoeProtein.c:135:2:  [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(pro->def, def);
data/snap-2013-11-29/Zoe/zoeProtein.c:136:2:  [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(pro->seq, seq);
data/snap-2013-11-29/Zoe/zoeState.c:65:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %f %f %d %d %s", state_name, &init, &term, &min, &max, duration) != 6) {
data/snap-2013-11-29/Zoe/zoeTools.c:59:8:  [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).
	(void)strcpy(PROGRAM_NAME, string);
data/snap-2013-11-29/Zoe/zoeTools.c:217:8:  [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.
	(void)vfprintf(stream, fmt, args);
data/snap-2013-11-29/Zoe/zoeTools.c:226:8:  [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.
	(void)vfprintf(stdout, fmt, args);
data/snap-2013-11-29/Zoe/zoeTools.c:235:8:  [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.
	(void)vfprintf(stderr, fmt, args);
data/snap-2013-11-29/Zoe/zoeTools.c:259:8:  [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.
	(void)vfprintf(stderr, fmt, args);
data/snap-2013-11-29/Zoe/zoeTools.c:270:8:  [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.
	(void)vfprintf(stderr, fmt, args);
data/snap-2013-11-29/Zoe/zoeTools.c:425:8:  [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).
	(void)strcpy(vec->elem[vec->size], text);
data/snap-2013-11-29/Zoe/zoeTools.c:873:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(command, "gunzip -c %s", name);
data/snap-2013-11-29/Zoe/zoeTools.c:874:17:  [4] (shell) popen:
  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.
		file.stream = popen(command, "r");
data/snap-2013-11-29/Zoe/zoeTools.c:878:2:  [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(file.name, name);
data/snap-2013-11-29/Zoe/zoeTransition.c:55:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(stream, "%s %s %f", from, to, &prob) != 3) {
data/snap-2013-11-29/Zoe/zoeTrellis.c:473:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(name, "%s-snap.%d", id, group);
data/snap-2013-11-29/Zoe/zoeTrellis.c:481:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
				sprintf(name, "%s-snap.%d", id, group);
data/snap-2013-11-29/fathom.c:786:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(token, "%s-%d from sequence %s", name, id, DNA->def);
data/snap-2013-11-29/fathom.c:1440:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(name, "region-%d (%s %d..%d)", span_count, DNA->def, start, end);
data/snap-2013-11-29/forge.c:287:9:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	while (fscanf(file.stream, "%s %d", id, &weight) != EOF) {
data/snap-2013-11-29/forge.c:344:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(filename, "%s-%d-%d.count", m->counts->name, m->order, m->length);
data/snap-2013-11-29/forge.c:350:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(filename, "%s-%d-%d.model", m->counts->name, m->order, m->length);
data/snap-2013-11-29/forge.c:572:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(filename, "%s-explicit.duration", name);
data/snap-2013-11-29/forge.c:605:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(filename, "%s-geometric.duration", name);
data/snap-2013-11-29/snap.c:123:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(option, "-N%s", name);
data/snap-2013-11-29/snap.c:130:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(option, "-A%s", name);
data/snap-2013-11-29/snap.c:178:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(option, "-N%s", name);
data/snap-2013-11-29/snap.c:185:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(option, "-A%s", name);
data/snap-2013-11-29/snap.c:201:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(option, "-%s", name);
data/snap-2013-11-29/snap.c:309:3:  [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(f->group, name);
data/snap-2013-11-29/snap.c:320:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		sprintf(path, "%s/HMM/%s", ZOE, name);
data/snap-2013-11-29/snap.c:325:6:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	if (fscanf(file, "%s", type) != 1) zoeExit("error checking HMM file");
data/snap-2013-11-29/snap.c:618:27:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		if (zoeOption("-name")) sprintf(name, "%s-%s.%d", id, zoeOption("-name"), i+1);
data/snap-2013-11-29/snap.c:619:27:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		else                    sprintf(name, "%s-snap.%d", id, i+1);
data/snap-2013-11-29/snap.c:626:3:  [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(gene->name, name);
data/snap-2013-11-29/snap.c:631:3:  [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(gene->tx->def, name);
data/snap-2013-11-29/snap.c:636:3:  [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(gene->aa->def, name);
data/snap-2013-11-29/Zoe/zoeHMM.c:495:20:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
	char   * ZOE    = getenv("ZOE");
data/snap-2013-11-29/Zoe/zoeIsochore.c:102:25:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
	char        * ZOE    = getenv("ZOE");
data/snap-2013-11-29/exonpairs.c:256:8:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
	ZOE = getenv("ZOE");
data/snap-2013-11-29/fathom.c:204:30:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	if (zoeOption("-randseed")) srand(atoi(zoeOption("-randseed")));
data/snap-2013-11-29/fathom.c:205:30:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	else                        srand(time(NULL));
data/snap-2013-11-29/snap.c:144:8:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
	ZOE = getenv("ZOE");
data/snap-2013-11-29/Zoe/lexica.c:44:2:  [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[8192], *token = NULL;
data/snap-2013-11-29/Zoe/lexica.c:66:14:  [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(argv[1], "r")) == NULL) zoeExit("file error (%s)", argv[1]);
data/snap-2013-11-29/Zoe/seqedit.c:74:21:  [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 ((stream = fopen(filename, "r") ) == NULL)
data/snap-2013-11-29/Zoe/seqedit.c:86:20:  [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).
		zoeLCsmooth(dna, atoi(zoeOption("-flank")), atoi(zoeOption("-island")),
data/snap-2013-11-29/Zoe/seqedit.c:86:47:  [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).
		zoeLCsmooth(dna, atoi(zoeOption("-flank")), atoi(zoeOption("-island")),
data/snap-2013-11-29/Zoe/seqedit.c:87:4:  [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).
			atoi(zoeOption("-min-len")));
data/snap-2013-11-29/Zoe/seqedit.c:108:13:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			cut    = atoi(zoeOption("-cut"));
data/snap-2013-11-29/Zoe/seqedit.c:109:13:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			length = atoi(zoeOption("-length"));
data/snap-2013-11-29/Zoe/twinkle.c:75:40:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-match"))      match = atoi(zoeOption("-match"));
data/snap-2013-11-29/Zoe/twinkle.c:76:43:  [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).
	if (zoeOption("-mismatch"))   mismatch = atoi(zoeOption("-mismatch"));
data/snap-2013-11-29/Zoe/twinkle.c:77:39:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-gap-init"))   gapI = atoi(zoeOption("-gap-init"));
data/snap-2013-11-29/Zoe/twinkle.c:78:39:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-gap-extend")) gapE = atoi(zoeOption("-gap-extend"));
data/snap-2013-11-29/Zoe/twinkle.c:79:40:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-score"))      score = atoi(zoeOption("-score"));
data/snap-2013-11-29/Zoe/twinkle.c:80:45:  [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).
	if (zoeOption("-memory"))     MAX_MEMORY = atoi(zoeOption("-memory"));
data/snap-2013-11-29/Zoe/zoe-loop.c:124:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (argc == 2) Iterations = atoi(argv[1]);
data/snap-2013-11-29/Zoe/zoe-loop.c:285:2:  [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     seq[8];
data/snap-2013-11-29/Zoe/zoeAlignment.c:736:2:  [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[256];
data/snap-2013-11-29/Zoe/zoeAlignment.c:745:14:  [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, "r")) == NULL) zoeExit("file error %s\n", filename);
data/snap-2013-11-29/Zoe/zoeCDS.c:47:14:  [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.
static const char S5P[5] = {'A', 'C', 'G', 'T', 'N'}; /* positive */
data/snap-2013-11-29/Zoe/zoeCDS.c:48:14:  [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.
static const char S5N[5] = {'T', 'G', 'C', 'A', 'N'}; /* negative */
data/snap-2013-11-29/Zoe/zoeCDS.c:77:2:  [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       text[256];
data/snap-2013-11-29/Zoe/zoeCDS.c:87:3:  [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(text, "gene:mixed_strands");
data/snap-2013-11-29/Zoe/zoeCDS.c:94:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		sprintf(text, "gene:unknown_strand");
data/snap-2013-11-29/Zoe/zoeCDS.c:115:3:  [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(text, "gene:multiple_Esngl");
data/snap-2013-11-29/Zoe/zoeCDS.c:119:3:  [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(text, "gene:multiple_Einit");
data/snap-2013-11-29/Zoe/zoeCDS.c:123:3:  [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(text, "gene:multiple_Eterm");
data/snap-2013-11-29/Zoe/zoeCDS.c:131:5:  [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(text, "gene:misordered_Einit");
data/snap-2013-11-29/Zoe/zoeCDS.c:136:5:  [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(text, "gene:misordered_Einit");
data/snap-2013-11-29/Zoe/zoeCDS.c:144:5:  [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(text, "gene:misordered_Eterm");
data/snap-2013-11-29/Zoe/zoeCDS.c:149:5:  [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(text, "gene:misordered_Eterm");
data/snap-2013-11-29/Zoe/zoeCDS.c:160:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "exon-%d:out_of_bounds", idx);
data/snap-2013-11-29/Zoe/zoeCDS.c:170:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "exon-%d:overlaps_prev_exon", idx);
data/snap-2013-11-29/Zoe/zoeCDS.c:173:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "exon-%d:abuts_prev_exon", idx);
data/snap-2013-11-29/Zoe/zoeCDS.c:200:3:  [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[estart], &dna->seq[exon->start], elength);
data/snap-2013-11-29/Zoe/zoeCDS.c:403:2:  [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 text[256];
data/snap-2013-11-29/Zoe/zoeCDS.c:435:3:  [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(text, "gene:no_exons");
data/snap-2013-11-29/Zoe/zoeCDS.c:479:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "split-start");
data/snap-2013-11-29/Zoe/zoeCDS.c:483:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "split-stop");
data/snap-2013-11-29/Zoe/zoeCDS.c:487:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "cds:incomplete");
data/snap-2013-11-29/Zoe/zoeCDS.c:524:3:  [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(text, "cds:internal_stop");
data/snap-2013-11-29/Zoe/zoeCDS.c:557:3:  [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(text, "gene:short(%d)", nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:561:3:  [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(text, "gene:long(%d)", nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:571:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "exon-%d:short(%d)", idx, nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:574:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "exon-%d:long(%d)", idx, nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:585:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "intron-%d:short(%d)", idx, nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:589:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(text, "intron-%d:long(%d)", idx, nt_length);
data/snap-2013-11-29/Zoe/zoeCDS.c:606:5:  [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(text, "intron-%d:%c%c..%c%c", idx, S5P[b1], S5P[b2], S5P[b3], S5P[b4]);
data/snap-2013-11-29/Zoe/zoeCDS.c:611:5:  [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(text, "intron-%d:%c%c..%c%c", idx, S5N[b4], S5N[b3], S5N[b2], S5N[b1]);
data/snap-2013-11-29/Zoe/zoeDNA.c:34:8:  [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.
static char s5CodonTable[5][5][5] = {
data/snap-2013-11-29/Zoe/zoeDNA.c:474:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(file, "r")) == NULL)
data/snap-2013-11-29/Zoe/zoeDistribution.c:60:8:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	(void)memcpy(d->param, param, params * sizeof(float));
data/snap-2013-11-29/Zoe/zoeDistribution.c:65:2:  [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                  func_name[32];
data/snap-2013-11-29/Zoe/zoeDistribution.c:66:2:  [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                  input[32];
data/snap-2013-11-29/Zoe/zoeDistribution.c:113:2:  [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 score[16];
data/snap-2013-11-29/Zoe/zoeDuration.c:74:2:  [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              duration_name[16];
data/snap-2013-11-29/Zoe/zoeDuration.c:107:2:  [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 label[16];
data/snap-2013-11-29/Zoe/zoeFastaFile.c:156:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(filename, "r")) == NULL) {
data/snap-2013-11-29/Zoe/zoeFeature.c:100:2:  [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[256], Label[64], Start[64], End[64], Strand[64], Score[64],
data/snap-2013-11-29/Zoe/zoeFeature.c:175:2:  [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[1024], Source[64], ID[64], Label[64],
data/snap-2013-11-29/Zoe/zoeFeature.c:214:2:  [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 label[16], start[16], end[16], strand[8], score[32],
data/snap-2013-11-29/Zoe/zoeFeature.c:234:2:  [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 label[16], start[16], end[16], strand[8], score[32],
data/snap-2013-11-29/Zoe/zoeFeature.c:255:2:  [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 label[16], start[16], end[16];
data/snap-2013-11-29/Zoe/zoeFeature.c:269:2:  [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 label[16], start[16], end[16], strand[8], score[32];
data/snap-2013-11-29/Zoe/zoeFeature.c:411:19:  [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.
		case None:      strcpy(string, "None");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:412:19:  [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.
		case Inter:     strcpy(string, "Inter");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:413:19:  [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.
		case Int0:      strcpy(string, "Int0");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:414:19:  [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.
		case Int1:      strcpy(string, "Int1");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:415:19:  [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.
		case Int1T:     strcpy(string, "Int1T");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:416:19:  [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.
		case Int2:      strcpy(string, "Int2");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:417:19:  [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.
		case Int2TA:    strcpy(string, "Int2TA");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:418:19:  [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.
		case Int2TG:    strcpy(string, "Int2TG");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:419:19:  [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.
		case Intron:    strcpy(string, "Intron");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:420:19:  [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.
		case UTR5:      strcpy(string, "UTR5");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:421:19:  [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.
		case UTR3:      strcpy(string, "UTR3");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:422:19:  [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.
		case Esngl:     strcpy(string, "Esngl");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:423:19:  [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.
		case Einit:     strcpy(string, "Einit");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:424:19:  [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.
		case Eterm:     strcpy(string, "Eterm");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:425:19:  [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.
		case Exon:      strcpy(string, "Exon");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:426:19:  [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.
		case Coding:    strcpy(string, "Coding");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:427:19:  [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.
		case Gene:      strcpy(string, "Gene");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:428:19:  [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.
		case Acceptor:  strcpy(string, "Acceptor");   break;
data/snap-2013-11-29/Zoe/zoeFeature.c:429:19:  [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.
		case Donor:     strcpy(string, "Donor");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:430:19:  [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.
		case Start:     strcpy(string, "Start");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:431:19:  [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.
		case Stop:      strcpy(string, "Stop");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:432:19:  [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.
		case Repeat:    strcpy(string, "Repeat");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:433:19:  [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.
		case CNS:       strcpy(string, "CNS");        break;
data/snap-2013-11-29/Zoe/zoeFeature.c:434:19:  [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.
		case ORF:       strcpy(string, "ORF");        break;
data/snap-2013-11-29/Zoe/zoeFeature.c:435:19:  [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.
		case PolyA:     strcpy(string, "PolyA");      break;
data/snap-2013-11-29/Zoe/zoeFeature.c:436:19:  [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.
		case Prom:      strcpy(string, "Prom");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:437:19:  [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.
		case BPS:       strcpy(string, "BPS");        break;
data/snap-2013-11-29/Zoe/zoeFeature.c:438:19:  [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.
		case TSS:       strcpy(string, "TSS");        break;
data/snap-2013-11-29/Zoe/zoeFeature.c:439:19:  [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.
		case Misc:      strcpy(string, "Misc");       break;
data/snap-2013-11-29/Zoe/zoeFeature.c:440:19:  [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.
		case HSP_NN:    strcpy(string, "HSP_NN");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:441:19:  [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.
		case HSP_NA:    strcpy(string, "HSP_NA");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:442:19:  [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.
		case HSP_AN:    strcpy(string, "HSP_AN");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:443:19:  [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.
		case HSP_AA:    strcpy(string, "HSP_AA");     break;
data/snap-2013-11-29/Zoe/zoeFeature.c:446:10:  [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.
			(void)strcpy(string, "Unknown");
data/snap-2013-11-29/Zoe/zoeFeature.c:451:2:  [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 string[32];
data/snap-2013-11-29/Zoe/zoeFeatureFactory.c:229:2:  [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          key[16];
data/snap-2013-11-29/Zoe/zoeFeatureFactory.c:231:2:  [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(key, "%d", pos);
data/snap-2013-11-29/Zoe/zoeFeatureFactory.c:390:2:  [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              key[16];
data/snap-2013-11-29/Zoe/zoeFeatureFactory.c:450:3:  [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(key, "%d", exon->end);
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:44:2:  [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         string[12]; /* ought to be big enough for whole genomes */
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:53:3:  [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(string, "%d", index);
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:227:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(file, "r")) == NULL)
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:340:2:  [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          string[12];
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:351:3:  [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(string, "%d", index);
data/snap-2013-11-29/Zoe/zoeHMM.c:56:2:  [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 tmp[32];
data/snap-2013-11-29/Zoe/zoeHMM.c:392:2:  [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     type[16];
data/snap-2013-11-29/Zoe/zoeHMM.c:393:2:  [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[256];
data/snap-2013-11-29/Zoe/zoeHMM.c:496:2:  [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     path[1024];
data/snap-2013-11-29/Zoe/zoeHMM.c:498:11:  [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).
	stream = fopen(file, "r");
data/snap-2013-11-29/Zoe/zoeHMM.c:501:12:  [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).
		stream = fopen(path, "r");
data/snap-2013-11-29/Zoe/zoeIsochore.c:75:2:  [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[256];
data/snap-2013-11-29/Zoe/zoeIsochore.c:103:2:  [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          path[1024];
data/snap-2013-11-29/Zoe/zoeIsochore.c:105:11:  [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).
	stream = fopen(file, "r");
data/snap-2013-11-29/Zoe/zoeIsochore.c:108:12:  [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).
		stream = fopen(path, "r");
data/snap-2013-11-29/Zoe/zoeModel.c:39:2:  [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     type[16];
data/snap-2013-11-29/Zoe/zoeModel.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     name[16];
data/snap-2013-11-29/Zoe/zoeModel.c:41:2:  [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     data[16];
data/snap-2013-11-29/Zoe/zoeModel.c:133:2:  [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 typestring[16];
data/snap-2013-11-29/Zoe/zoeModel.c:134:2:  [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 data[16];
data/snap-2013-11-29/Zoe/zoeModel.c:138:13:  [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.
		case WMM: strcpy(typestring, "WMM"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:139:13:  [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.
		case LUT: strcpy(typestring, "LUT"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:140:13:  [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.
		case SAM: strcpy(typestring, "SAM"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:141:13:  [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.
		case SDT: strcpy(typestring, "SDT"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:142:13:  [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.
		case CDS: strcpy(typestring, "CDS"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:143:13:  [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.
		case MIX: strcpy(typestring, "MIX"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:144:13:  [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.
		case TRM: strcpy(typestring, "TRM"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:145:13:  [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.
		default:  strcpy(typestring, "???"); break;
data/snap-2013-11-29/Zoe/zoeModel.c:191:9:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
	file = tmpfile();
data/snap-2013-11-29/Zoe/zoeModel.c:264:2:  [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      string[50];
data/snap-2013-11-29/Zoe/zoeModel.c:312:2:  [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      string[50];
data/snap-2013-11-29/Zoe/zoeModel.c:364:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(file, "r")) == NULL)
data/snap-2013-11-29/Zoe/zoeModel.c:377:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(file, "r")) == NULL)
data/snap-2013-11-29/Zoe/zoeModel.c:423:2:  [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 text[256];
data/snap-2013-11-29/Zoe/zoeModel.c:427:11:  [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.
	bytes += sprintf(text, "Coding CDS 3 2 4 3 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:428:11:  [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.
	bytes += sprintf(text+bytes, "\tframe0 LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:429:11:  [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.
	bytes += sprintf(text+bytes, "\tframe1 LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:430:11:  [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.
	bytes += sprintf(text+bytes, "\tframe2 LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:435:2:  [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 text[64];
data/snap-2013-11-29/Zoe/zoeModel.c:437:2:  [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(text, "Intron LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:442:2:  [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 text[64];
data/snap-2013-11-29/Zoe/zoeModel.c:444:2:  [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(text, "Inter LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:449:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:453:11:  [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.
	bytes += sprintf(text, "Acceptor SDT 2 1 4 2 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:455:12:  [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.
		bytes += sprintf(text+bytes, "\tAG WMM %d %d 4 0 0\n", length, length -4);
data/snap-2013-11-29/Zoe/zoeModel.c:457:12:  [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.
		bytes += sprintf(text+bytes, "\tAG SAM %d %d 4 %d 0\n", length, length -4, length);
data/snap-2013-11-29/Zoe/zoeModel.c:459:38:  [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.
			if      (length -i == 5) bytes += sprintf(text+bytes, "\t\tA LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:460:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (length -i == 4) bytes += sprintf(text+bytes, "\t\tG LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:461:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (length -i >  3) bytes += sprintf(text+bytes, "\t\tI-%d LUT %d %d 4 0 0\n", length -i -3, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:462:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else                     bytes += sprintf(text+bytes, "\t\tE+%d LUT %d %d 4 0 0\n", i -length +4, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:465:11:  [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.
	bytes += sprintf(text+bytes, "\tNN TRM 0 0 0 0 0\n");
data/snap-2013-11-29/Zoe/zoeModel.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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:475:11:  [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.
	bytes += sprintf(text, "Donor SDT 2 0 4 2 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:477:12:  [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.
		bytes += sprintf(text+bytes, "\tGT WMM %d 3 4 0 0\n", length);
data/snap-2013-11-29/Zoe/zoeModel.c:479:12:  [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.
		bytes += sprintf(text+bytes, "\tGT SAM %d 3 4 %d 0\n", length, length);
data/snap-2013-11-29/Zoe/zoeModel.c:481:30:  [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.
			if      (i == 3) bytes += sprintf(text+bytes, "\t\tG LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:482:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (i == 4) bytes += sprintf(text+bytes, "\t\tT LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:483:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (i <  3) bytes += sprintf(text+bytes, "\t\tE-%d LUT %d %d 4 0 0\n", 3 -i, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:484:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else             bytes += sprintf(text+bytes, "\t\tI+%d LUT %d %d 4 0 0\n", i -4, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:487:11:  [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.
	bytes += sprintf(text+bytes, "\tNN TRM 0 0 0 0 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:494:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:498:11:  [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.
	bytes += sprintf(text+bytes, "Start SDT 3 0 4 2 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:500:12:  [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.
		bytes += sprintf(text+bytes, "\tATG WMM %d %d 4 0 0\n", length, length -6);
data/snap-2013-11-29/Zoe/zoeModel.c:502:12:  [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.
		bytes += sprintf(text+bytes, "\tATG SAM %d %d 4 %d 0\n", length, length -6, length);
data/snap-2013-11-29/Zoe/zoeModel.c:504:38:  [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.
			if      (length -i == 6) bytes += sprintf(text+bytes, "\t\tA LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:505:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (length -i == 5) bytes += sprintf(text+bytes, "\t\tT LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:506:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (length -i == 4) bytes += sprintf(text+bytes, "\t\tG LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:507:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else if (length -i >  3) bytes += sprintf(text+bytes, "\t\tN-%d LUT %d %d 4 0 0\n", length -i -6, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:508:38:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			else                     bytes += sprintf(text+bytes, "\t\tE+%d LUT %d %d 4 0 0\n", i -length +4, order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:511:11:  [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.
	bytes += sprintf(text+bytes, "\tNNN TRM 0 0 0 0 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:517:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:520:11:  [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.
	bytes += sprintf(text, "Stop SDT 3 0 4 4 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:521:11:  [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.
	bytes += sprintf(text+bytes, "\tTAA WMM %d 6 4 0 0\n", length);
data/snap-2013-11-29/Zoe/zoeModel.c:522:11:  [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.
	bytes += sprintf(text+bytes, "\tTAG WMM %d 6 4 0 0\n", length);
data/snap-2013-11-29/Zoe/zoeModel.c:523:11:  [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.
	bytes += sprintf(text+bytes, "\tTGA WMM %d 6 4 0 0\n", length);
data/snap-2013-11-29/Zoe/zoeModel.c:524:11:  [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.
	bytes += sprintf(text+bytes, "\tNNN TRM 0 0 0 0 0\n");
data/snap-2013-11-29/Zoe/zoeModel.c:538:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:540:2:  [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(text, "UTR5 LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:545:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:547:2:  [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(text, "UTR3 LUT %d %d 4 0 0\n", order +1, order);
data/snap-2013-11-29/Zoe/zoeModel.c:552:2:  [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 text[8192];
data/snap-2013-11-29/Zoe/zoeModel.c:557:12:  [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.
		bytes += sprintf(text, "PolyA WMM %d 0 4 0 0\n", length);
data/snap-2013-11-29/Zoe/zoeModel.c:559:12:  [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.
		bytes += sprintf(text, "PolyA SAM %d 0 4 %d 0\n", length, length);
data/snap-2013-11-29/Zoe/zoeModel.c:561:13:  [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.
			bytes += sprintf(text+bytes, "\t\t%d LUT %d %d 4 0 0\n", i, order +1, order);
data/snap-2013-11-29/Zoe/zoeProtein.c:167:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	if ((stream = fopen(file, "r")) == NULL)
data/snap-2013-11-29/Zoe/zoeState.c:57:2:  [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         state_name[16];
data/snap-2013-11-29/Zoe/zoeState.c:58:2:  [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         duration[16];
data/snap-2013-11-29/Zoe/zoeState.c:111:2:  [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[16];
data/snap-2013-11-29/Zoe/zoeTools.c:56:8:  [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.
static char PROGRAM_NAME[256] = "unnamed program";
data/snap-2013-11-29/Zoe/zoeTools.c:135:2:  [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, "%d", n);
data/snap-2013-11-29/Zoe/zoeTools.c:140:35:  [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.
	if (val == UNDEFINED_COOR) (void)strcpy(s, "...");
data/snap-2013-11-29/Zoe/zoeTools.c:176:35:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	else                       (void)sprintf(s, "%.3f", val);
data/snap-2013-11-29/Zoe/zoeTools.c:824:11:  [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).
	stream = fopen(filename, "r");
data/snap-2013-11-29/Zoe/zoeTools.c:858:2:  [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    command[1024];
data/snap-2013-11-29/Zoe/zoeTools.c:871:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		file.stream = fopen(name, "r");
data/snap-2013-11-29/Zoe/zoeTools.h:178:2:  [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[1024];
data/snap-2013-11-29/Zoe/zoeTransition.c:51:2:  [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  from[16];
data/snap-2013-11-29/Zoe/zoeTransition.c:52:2:  [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  to[16];
data/snap-2013-11-29/Zoe/zoeTransition.c:63:2:  [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 from[16];
data/snap-2013-11-29/Zoe/zoeTransition.c:64:2:  [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 to[16];
data/snap-2013-11-29/Zoe/zoeTrellis.c:458:2:  [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            id[64], name[256];
data/snap-2013-11-29/Zoe/zoeTrellis.c:630:2:  [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[32];
data/snap-2013-11-29/exonpairs.c:110:2:  [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 seq1[FLANK_LENGTH +1], seq2[FLANK_LENGTH +1];
data/snap-2013-11-29/exonpairs.c:111:2:  [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 location[64];
data/snap-2013-11-29/exonpairs.c:123:2:  [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(location, "%d-%d", e1->end, e2->start);
data/snap-2013-11-29/exonpairs.c:243:54:  [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).
	if (zoeOption("-min-intron"))   MIN_INTRON_LENGTH = atoi(zoeOption("-min-intron"));
data/snap-2013-11-29/exonpairs.c:244:54:  [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).
	if (zoeOption("-max-intron"))   MAX_INTRON_LENGTH = atoi(zoeOption("-max-intron"));
data/snap-2013-11-29/exonpairs.c:245:54:  [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).
	if (zoeOption("-einit-length")) MIN_EINIT_LENGTH  = atoi(zoeOption("-einit-length"));
data/snap-2013-11-29/exonpairs.c:246:54:  [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).
	if (zoeOption("-eterm-length")) MIN_ETERM_LENGTH  = atoi(zoeOption("-eterm-length"));
data/snap-2013-11-29/exonpairs.c:247:54:  [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).
	if (zoeOption("-exon-length"))  MIN_EXON_LENGTH   = atoi(zoeOption("-exon-length"));
data/snap-2013-11-29/exonpairs.c:253:54:  [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).
	if (zoeOption("-flank-length")) FLANK_LENGTH      = atoi(zoeOption("-flank-length"));
data/snap-2013-11-29/fathom.c:204:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-randseed")) srand(atoi(zoeOption("-randseed")));
data/snap-2013-11-29/fathom.c:207:48:  [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).
	if (zoeOption("-min-intron")) zoeSetMinIntron(atoi(zoeOption("-min-intron")));	
data/snap-2013-11-29/fathom.c:208:48:  [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).
	if (zoeOption("-max-intron")) zoeSetMaxIntron(atoi(zoeOption("-max-intron")));
data/snap-2013-11-29/fathom.c:209:46:  [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).
	if (zoeOption("-min-exon"))   zoeSetMinExon(atoi(zoeOption("-min-exon")));	
data/snap-2013-11-29/fathom.c:210:46:  [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).
	if (zoeOption("-max-exon"))   zoeSetMaxExon(atoi(zoeOption("-max-exon")));
data/snap-2013-11-29/fathom.c:211:46:  [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).
	if (zoeOption("-min-gene"))   zoeSetMinGene(atoi(zoeOption("-min-gene")));	
data/snap-2013-11-29/fathom.c:212:46:  [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).
	if (zoeOption("-max-gene"))   zoeSetMaxGene(atoi(zoeOption("-max-gene")));
data/snap-2013-11-29/fathom.c:213:45:  [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).
	if (zoeOption("-min-cds"))    zoeSetMinCDS(atoi(zoeOption("-min-cds")));	
data/snap-2013-11-29/fathom.c:214:45:  [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).
	if (zoeOption("-max-cds"))    zoeSetMaxCDS(atoi(zoeOption("-max-cds")));
data/snap-2013-11-29/fathom.c:238:12:  [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).
	DNA_out = fopen("anti.dna", "w");
data/snap-2013-11-29/fathom.c:239:12:  [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).
	ANN_out = fopen("anti.ann", "w");
data/snap-2013-11-29/fathom.c:258:12:  [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).
	DNA_out = fopen("fuse.dna", "w");
data/snap-2013-11-29/fathom.c:259:12:  [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).
	ANN_out = fopen("fuse.ann", "w");
data/snap-2013-11-29/fathom.c:261:15:  [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).
	group_size = atoi(zoeOption("-fuse"));
data/snap-2013-11-29/fathom.c:428:2:  [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 *  nt[5] = {"A", "C", "G", "T", "N"};
data/snap-2013-11-29/fathom.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 *  dd[25] = {
data/snap-2013-11-29/fathom.c:606:2:  [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 filename[256];
data/snap-2013-11-29/fathom.c:609:10:  [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).
	split = atoi(zoeOption("-number"));
data/snap-2013-11-29/fathom.c:619:3:  [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(filename, "%d.dna", i);
data/snap-2013-11-29/fathom.c:620:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((dna[i] = fopen(filename, "w")) == NULL) zoeExit("error opening %s", filename);
data/snap-2013-11-29/fathom.c:621:3:  [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(filename, "%d.ann", i);
data/snap-2013-11-29/fathom.c:622:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((ann[i] = fopen(filename, "w")) == NULL) zoeExit("error opening %s", filename);
data/snap-2013-11-29/fathom.c:664:20:  [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).
		if ((train_dna = fopen("train.dna", "w")) == NULL) zoeExit("can't open train.dna");
data/snap-2013-11-29/fathom.c:665:20:  [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).
		if ((train_ann = fopen("train.ann", "w")) == NULL) zoeExit("can't open train.ann");
data/snap-2013-11-29/fathom.c:666:20:  [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).
		if ((test_dna  = fopen("test.dna",  "w")) == NULL) zoeExit("can't open test.dna");
data/snap-2013-11-29/fathom.c:667:20:  [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).
		if ((test_ann  = fopen("test.ann",  "w")) == NULL) zoeExit("can't open test.ann");
data/snap-2013-11-29/fathom.c:669:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((hi_dna = fopen("hi-gc.dna", "w")) == NULL) zoeExit("can't open hi-gc.dna");
data/snap-2013-11-29/fathom.c:670:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((hi_ann = fopen("hi-gc.ann", "w")) == NULL) zoeExit("can't open hi-gc.ann");
data/snap-2013-11-29/fathom.c:671:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((lo_dna = fopen("lo-gc.dna", "w")) == NULL) zoeExit("can't open lo-gc.dna");
data/snap-2013-11-29/fathom.c:672:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((lo_ann = fopen("lo-gc.ann", "w")) == NULL) zoeExit("can't open lo-gc.ann");
data/snap-2013-11-29/fathom.c:723:2:  [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, token[64];
data/snap-2013-11-29/fathom.c:739:13:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			length = atoi(zoeOption("-length"));
data/snap-2013-11-29/fathom.c:740:13:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			offset = atoi(zoeOption("-offset"));
data/snap-2013-11-29/fathom.c:863:37:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-offset")) offset = atoi(zoeOption("-offset"));
data/snap-2013-11-29/fathom.c:866:37:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-length")) length = atoi(zoeOption("-length"));
data/snap-2013-11-29/fathom.c:902:37:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-offset")) offset = atoi(zoeOption("-offset"));
data/snap-2013-11-29/fathom.c:905:37:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-length")) length = atoi(zoeOption("-length"));
data/snap-2013-11-29/fathom.c:1175:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	padding = atoi(zoeOption("-export"));
data/snap-2013-11-29/fathom.c:1182:20:  [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).
	if ((dna_stream = fopen("export.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1183:20:  [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).
	if ((ann_stream = fopen("export.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1184:20:  [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).
	if ((tx_stream  = fopen("export.tx",  "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1185:20:  [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).
	if ((aa_stream  = fopen("export.aa",  "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1385:2:  [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              category, name[1024];
data/snap-2013-11-29/fathom.c:1393:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	padding = atoi(zoeOption("-categorize"));
data/snap-2013-11-29/fathom.c:1395:15:  [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 ((e_dna = fopen("err.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1396:15:  [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 ((e_ann = fopen("err.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1397:15:  [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 ((w_dna = fopen("wrn.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1398:15:  [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 ((w_ann = fopen("wrn.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1399:15:  [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 ((a_dna = fopen("alt.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1400:15:  [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 ((a_ann = fopen("alt.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1401:15:  [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 ((o_dna = fopen("olp.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1402:15:  [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 ((o_ann = fopen("olp.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1403:15:  [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 ((u_dna = fopen("uni.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1404:15:  [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 ((u_ann = fopen("uni.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1498:41:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-upstream")) upstream = atoi(zoeOption("-upstream"));
data/snap-2013-11-29/fathom.c:1500:45:  [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).
	if (zoeOption("-downstream")) downstream = atoi(zoeOption("-downstream"));
data/snap-2013-11-29/fathom.c:1503:20:  [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).
	if ((dna_stream = fopen("export-feature.dna", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1504:20:  [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).
	if ((ann_stream = fopen("export-feature.ann", "w")) == NULL) zoeExit("file open error");
data/snap-2013-11-29/fathom.c:1583:15:  [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).
	min_length = atoi(zoeOption("-min-length"));
data/snap-2013-11-29/fathom.c:1716:2:  [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              string[64];
data/snap-2013-11-29/fathom.c:1731:3:  [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(string, "%d %d %c", f->start, f->end, f->strand);
data/snap-2013-11-29/fathom.c:1738:3:  [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(string, "%d %d %c", f->start, f->end, f->strand);
data/snap-2013-11-29/fathom.c:1845:2:  [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[16];
data/snap-2013-11-29/forge.c:197:45:  [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).
	if (zoeOption("-min-counts")) MIN_COUNTS = atoi(zoeOption("-min-counts"));
data/snap-2013-11-29/forge.c:201:47:  [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).
	if (zoeOption("-utr5-length")) UTR5_Length = atoi(zoeOption("-utr5-length"));
data/snap-2013-11-29/forge.c:202:47:  [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).
	if (zoeOption("-utr5-offset")) UTR5_Offset = atoi(zoeOption("-utr5-offset"));
data/snap-2013-11-29/forge.c:203:47:  [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).
	if (zoeOption("-utr3-length")) UTR3_Length = atoi(zoeOption("-utr3-length"));
data/snap-2013-11-29/forge.c:204:47:  [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).
	if (zoeOption("-utr3-offset")) UTR3_Offset = atoi(zoeOption("-utr3-offset"));
data/snap-2013-11-29/forge.c:205:40:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-polyA")) POLYA_LOOK = atoi(zoeOption("-polyA"));
data/snap-2013-11-29/forge.c:224:45:  [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).
	if (zoeOption("-min-intron")) MIN_INTRON = atoi(zoeOption("-min-intron"));
data/snap-2013-11-29/forge.c:279:2:  [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    id[64];
data/snap-2013-11-29/forge.c:336:2:  [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 filename[256];
data/snap-2013-11-29/forge.c:345:10:  [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, "w");
data/snap-2013-11-29/forge.c:351:10:  [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, "w");
data/snap-2013-11-29/forge.c:495:9:  [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("transitions", "w");
data/snap-2013-11-29/forge.c:553:2:  [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    filename[1024];
data/snap-2013-11-29/forge.c:554:2:  [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[64];
data/snap-2013-11-29/forge.c:573:9:  [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, "w");
data/snap-2013-11-29/forge.c:606:9:  [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, "w");
data/snap-2013-11-29/forge.c:663:38:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	if (zoeOption("-explicit")) fixed = atoi(zoeOption("-explicit"));
data/snap-2013-11-29/forge.c:765:12:  [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("phaseprefs", "w");
data/snap-2013-11-29/hmm-info.c:98:2:  [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[16];
data/snap-2013-11-29/hmm-info.c:101:11:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	length = atoi(zoeOption("-durations"));
data/snap-2013-11-29/hmm-info.c:109:5:  [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(name, "Intron");
data/snap-2013-11-29/snap.c:87:2:  [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            option[20], name[16];
data/snap-2013-11-29/snap.c:156:44:  [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).
	if (zoeOption("-min-cds")) SNAP_MIN_CDS = atoi(zoeOption("-min-cds"));
data/snap-2013-11-29/snap.c:210:20:  [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).
		if ((aa_stream = fopen(zoeOption("-aa"), "w")) == NULL) {
data/snap-2013-11-29/snap.c:215:20:  [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).
		if ((tx_stream = fopen(zoeOption("-tx"), "w")) == NULL) {
data/snap-2013-11-29/snap.c:225:20:  [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).
		if ((xd_stream = fopen(zoeOption("-xdef"), "r")) == NULL)
data/snap-2013-11-29/snap.c:315:2:  [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   type[64];
data/snap-2013-11-29/snap.c:316:2:  [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   path[1024];
data/snap-2013-11-29/snap.c:318:9:  [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(name, "r");
data/snap-2013-11-29/snap.c:321:10:  [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(path, "r");
data/snap-2013-11-29/snap.c:449:2:  [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 u0[16], u1[16], u2[16], a0[16], a1[16], a2[16];
data/snap-2013-11-29/snap.c:502:2:  [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   id[64], name[256];
data/snap-2013-11-29/Zoe/lexica.c:70:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		len = strlen(line);
data/snap-2013-11-29/Zoe/twinkle.c:82:19:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	if (match < 1 || mismatch < 1 || gapI < 1 || gapE < 1 || score < 1) {
data/snap-2013-11-29/Zoe/twinkle.c:91:39:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	HSPs = zoeAlign02(dna1, dna2, match, mismatch, gapI, gapE, score);
data/snap-2013-11-29/Zoe/zoeAlignment.c:162:30:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	if (hsp->match >= 0 && hsp->mismatch >= 0) {
data/snap-2013-11-29/Zoe/zoeAlignment.c:163:43:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		zoeS(stream, " %d/%d", hsp->match, hsp->mismatch);
data/snap-2013-11-29/Zoe/zoeAlignment.c:180:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	length = strlen(hsp->q_aln);
data/snap-2013-11-29/Zoe/zoeAlignment.c:189:18:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	hsp->mismatch = mismatch;
data/snap-2013-11-29/Zoe/zoeAlignment.c:228:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	length = strlen(string);
data/snap-2013-11-29/Zoe/zoeAlignment.h:48:11:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	int      mismatch;
data/snap-2013-11-29/Zoe/zoeCDS.c:204:6:  [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(seq) != nt_length) zoeExit("transcribe fatal error");
data/snap-2013-11-29/Zoe/zoeCDS.c:411:28:  [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).
	cds->name     = zoeMalloc(strlen(name) + 1); strcpy(cds->name, name);
data/snap-2013-11-29/Zoe/zoeDNA.c:117:16:  [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).
	dna->length = strlen(seq);	
data/snap-2013-11-29/Zoe/zoeDNA.c:121:26:  [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).
	dna->def    = zoeMalloc(strlen(def) +1);
data/snap-2013-11-29/Zoe/zoeDNA.c:461:15:  [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).
	if (dna->def[strlen(dna->def) -1] != '\n') zoeS(stream, "\n");
data/snap-2013-11-29/Zoe/zoeFastaFile.c:52:25:  [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).
	ff->def    = zoeMalloc(strlen(def) + 1);
data/snap-2013-11-29/Zoe/zoeFastaFile.c:53:25:  [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).
	ff->seq    = zoeMalloc(strlen(seq) + 1);
data/snap-2013-11-29/Zoe/zoeFastaFile.c:54:15:  [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).
	ff->length = strlen(seq);
data/snap-2013-11-29/Zoe/zoeFastaFile.c:70:6:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	c = fgetc(stream);
data/snap-2013-11-29/Zoe/zoeFastaFile.c:85:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stream))) {
data/snap-2013-11-29/Zoe/zoeFastaFile.c:105:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stream))) {
data/snap-2013-11-29/Zoe/zoeFastaFile.c:143:17:  [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).
	if (entry->def[strlen(entry->def) -1] != '\n') zoeS(stream, "\n");
data/snap-2013-11-29/Zoe/zoeFeature.c:73:24:  [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).
		f->group = zoeMalloc(strlen(group) +1);
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:115:22:  [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).
	ft->def = zoeMalloc(strlen(def) +1);
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:139:6:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	c = fgetc(stream);
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:154:14:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	while ((c = fgetc(stream)) != EOF) {
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:167:14:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	while ((c = fgetc(stream)) != EOF) {
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:192:14:  [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).
	if (ft->def[strlen(ft->def) -1] != '\n') zoeS(stream, "\n");
data/snap-2013-11-29/Zoe/zoeFeatureTable.c:203:14:  [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).
	if (ft->def[strlen(ft->def) -1] != '\n') zoeS(stream, "\n");
data/snap-2013-11-29/Zoe/zoeHMM.c:408:31:  [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).
	hmm->name        = zoeMalloc(strlen(name) + 1);
data/snap-2013-11-29/Zoe/zoeMath.c:103:18:  [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).
	for (i = 0, j = strlen(s) -1; i < j; i++, j--) {
data/snap-2013-11-29/Zoe/zoeMath.c:116:8:  [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).
	len = strlen(s);
data/snap-2013-11-29/Zoe/zoeModel.c:60:26:  [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).
	model->name = zoeMalloc(strlen(name) + 1);
data/snap-2013-11-29/Zoe/zoeModel.c:341:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
			for (j = 0; j < strlen(string); j++) {
data/snap-2013-11-29/Zoe/zoeProtein.c:113:16:  [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).
	pro->length = strlen(seq);
data/snap-2013-11-29/Zoe/zoeProtein.c:114:26:  [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).
	pro->def    = zoeMalloc(strlen(def) +1);
data/snap-2013-11-29/Zoe/zoeProtein.c:119:18:  [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).
	for (i = 0; i < strlen(seq); i++) {
data/snap-2013-11-29/Zoe/zoeProtein.c:131:16:  [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).
	pro->length = strlen(seq);
data/snap-2013-11-29/Zoe/zoeProtein.c:132:26:  [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).
	pro->def    = zoeMalloc(strlen(def) +1);
data/snap-2013-11-29/Zoe/zoeProtein.c:138:18:  [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).
	for (i = 0; i < strlen(seq); i++) {
data/snap-2013-11-29/Zoe/zoeProtein.c:153:15:  [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).
	if (pro->def[strlen(pro->def) -1] != '\n') zoeS(stream, "\n");
data/snap-2013-11-29/Zoe/zoeTools.c:98:26:  [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).
		if (token[0] == '-' && strlen(token) > 1) {
data/snap-2013-11-29/Zoe/zoeTools.c:157:36:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	if (val == UNDEFINED_FRAME) (void)strcpy(s, ".");
data/snap-2013-11-29/Zoe/zoeTools.c:174:35:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	     if (val <= MIN_SCORE) (void)strcpy(s, ".");
data/snap-2013-11-29/Zoe/zoeTools.c:175:35:  [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.
	else if (val >= MAX_SCORE) (void)strcpy(s, "*");
data/snap-2013-11-29/Zoe/zoeTools.c:194:29:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	if      (val == '+') (void)strcpy(s, "+");
data/snap-2013-11-29/Zoe/zoeTools.c:195:29:  [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.
	else if (val == '-') (void)strcpy(s, "-");
data/snap-2013-11-29/Zoe/zoeTools.c:196:29:  [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.
	else                 (void)strcpy(s, ".");
data/snap-2013-11-29/Zoe/zoeTools.c:424:35:  [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).
	vec->elem[vec->size] = zoeMalloc(strlen(text) +1);
data/snap-2013-11-29/Zoe/zoeTools.c:500:18:  [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).
	for (i = 0; i < strlen(key); i++) {
data/snap-2013-11-29/Zoe/zoeTools.c:738:8:  [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).
	len = strlen(string);
data/snap-2013-11-29/Zoe/zoeTools.c:777:8:  [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).
	len = strlen(string);
data/snap-2013-11-29/Zoe/zoeTools.c:821:15:  [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).
	int length = strlen(filename);
data/snap-2013-11-29/Zoe/zoeTrellis.c:464:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(id, def, 63);
data/snap-2013-11-29/Zoe/zoeTrellis.c:465:18:  [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).
	for (i = 0; i < strlen(id); i++) {
data/snap-2013-11-29/exonpairs.c:115:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(seq1, dna->seq + start, FLANK_LENGTH);
data/snap-2013-11-29/exonpairs.c:119:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(seq2, dna->seq + start, FLANK_LENGTH);
data/snap-2013-11-29/snap.c:308:24:  [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).
		f->group = zoeMalloc(strlen(name) +1);
data/snap-2013-11-29/snap.c:458:4:  [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(u0, ".");
data/snap-2013-11-29/snap.c:459:4:  [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(u1, ".");
data/snap-2013-11-29/snap.c:460:4:  [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(u2, ".");
data/snap-2013-11-29/snap.c:467:4:  [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(a0, ".");
data/snap-2013-11-29/snap.c:468:4:  [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(a1, ".");
data/snap-2013-11-29/snap.c:469:4:  [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(a2, ".");
data/snap-2013-11-29/snap.c:609:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(id, plus_dna->def, 63);
data/snap-2013-11-29/snap.c:610:18:  [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).
	for (i = 0; i < strlen(plus_dna->def); i++) {
data/snap-2013-11-29/snap.c:625:26:  [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).
		gene->name = zoeMalloc(strlen(name) +1);
data/snap-2013-11-29/snap.c:630:29:  [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).
		gene->tx->def = zoeMalloc(strlen(name) +1);
data/snap-2013-11-29/snap.c:635:29:  [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).
		gene->aa->def = zoeMalloc(strlen(name) +1);

ANALYSIS SUMMARY:

Hits = 447
Lines analyzed = 16486 in approximately 0.57 seconds (29159 lines/second)
Physical Source Lines of Code (SLOC) = 11656
Hits@level = [0]  14 [1]  68 [2] 308 [3]   6 [4]  65 [5]   0
Hits@level+ = [0+] 461 [1+] 447 [2+] 379 [3+]  71 [4+]  65 [5+]   0
Hits/KSLOC@level+ = [0+] 39.5504 [1+] 38.3493 [2+] 32.5154 [3+] 6.09128 [4+] 5.57653 [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.