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/squizz-0.99d+dfsg/lib/compat/err.h
Examining data/squizz-0.99d+dfsg/lib/align/clustal.h
Examining data/squizz-0.99d+dfsg/lib/align/fasta2.h
Examining data/squizz-0.99d+dfsg/lib/align/mega.h
Examining data/squizz-0.99d+dfsg/lib/align/msf.h
Examining data/squizz-0.99d+dfsg/lib/align/nexusi.h
Examining data/squizz-0.99d+dfsg/lib/align/phylipi.h
Examining data/squizz-0.99d+dfsg/lib/align/phylips.h
Examining data/squizz-0.99d+dfsg/lib/align/stock.h
Examining data/squizz-0.99d+dfsg/lib/align/parse.h
Examining data/squizz-0.99d+dfsg/lib/align/phylip.h
Examining data/squizz-0.99d+dfsg/lib/align/clustall.c
Examining data/squizz-0.99d+dfsg/lib/align/clustaly.c
Examining data/squizz-0.99d+dfsg/lib/align/clustaly.h
Examining data/squizz-0.99d+dfsg/lib/align/megal.c
Examining data/squizz-0.99d+dfsg/lib/align/megay.c
Examining data/squizz-0.99d+dfsg/lib/align/megay.h
Examining data/squizz-0.99d+dfsg/lib/align/msfl.c
Examining data/squizz-0.99d+dfsg/lib/align/msfy.c
Examining data/squizz-0.99d+dfsg/lib/align/msfy.h
Examining data/squizz-0.99d+dfsg/lib/align/nexusil.c
Examining data/squizz-0.99d+dfsg/lib/align/nexusiy.c
Examining data/squizz-0.99d+dfsg/lib/align/nexusiy.h
Examining data/squizz-0.99d+dfsg/lib/align/phylipil.c
Examining data/squizz-0.99d+dfsg/lib/align/phylipiy.c
Examining data/squizz-0.99d+dfsg/lib/align/phylipiy.h
Examining data/squizz-0.99d+dfsg/lib/align/phylipsl.c
Examining data/squizz-0.99d+dfsg/lib/align/phylipsy.c
Examining data/squizz-0.99d+dfsg/lib/align/phylipsy.h
Examining data/squizz-0.99d+dfsg/lib/align/stockl.c
Examining data/squizz-0.99d+dfsg/lib/align/stocky.c
Examining data/squizz-0.99d+dfsg/lib/align/stocky.h
Examining data/squizz-0.99d+dfsg/lib/align/clustal.c
Examining data/squizz-0.99d+dfsg/lib/align/fasta2.c
Examining data/squizz-0.99d+dfsg/lib/align/mega.c
Examining data/squizz-0.99d+dfsg/lib/align/msf.c
Examining data/squizz-0.99d+dfsg/lib/align/nexusi.c
Examining data/squizz-0.99d+dfsg/lib/align/phylipi.c
Examining data/squizz-0.99d+dfsg/lib/align/phylips.c
Examining data/squizz-0.99d+dfsg/lib/align/stock.c
Examining data/squizz-0.99d+dfsg/lib/align/parse.c
Examining data/squizz-0.99d+dfsg/lib/align/phylip.c
Examining data/squizz-0.99d+dfsg/lib/extern/text.h
Examining data/squizz-0.99d+dfsg/lib/extern/file.h
Examining data/squizz-0.99d+dfsg/lib/extern/text.c
Examining data/squizz-0.99d+dfsg/lib/extern/file.c
Examining data/squizz-0.99d+dfsg/lib/sequence/embl.h
Examining data/squizz-0.99d+dfsg/lib/sequence/fasta.h
Examining data/squizz-0.99d+dfsg/lib/sequence/genbank.h
Examining data/squizz-0.99d+dfsg/lib/sequence/gcg.h
Examining data/squizz-0.99d+dfsg/lib/sequence/gde.h
Examining data/squizz-0.99d+dfsg/lib/sequence/ig.h
Examining data/squizz-0.99d+dfsg/lib/sequence/nbrf.h
Examining data/squizz-0.99d+dfsg/lib/sequence/codata.h
Examining data/squizz-0.99d+dfsg/lib/sequence/raw.h
Examining data/squizz-0.99d+dfsg/lib/sequence/sprot.h
Examining data/squizz-0.99d+dfsg/lib/sequence/parse.h
Examining data/squizz-0.99d+dfsg/lib/sequence/protein.h
Examining data/squizz-0.99d+dfsg/lib/sequence/utils.h
Examining data/squizz-0.99d+dfsg/lib/sequence/codatal.c
Examining data/squizz-0.99d+dfsg/lib/sequence/codatay.c
Examining data/squizz-0.99d+dfsg/lib/sequence/codatay.h
Examining data/squizz-0.99d+dfsg/lib/sequence/embll.c
Examining data/squizz-0.99d+dfsg/lib/sequence/embly.c
Examining data/squizz-0.99d+dfsg/lib/sequence/embly.h
Examining data/squizz-0.99d+dfsg/lib/sequence/fastal.c
Examining data/squizz-0.99d+dfsg/lib/sequence/fastay.c
Examining data/squizz-0.99d+dfsg/lib/sequence/fastay.h
Examining data/squizz-0.99d+dfsg/lib/sequence/gcgl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gcgy.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gcgy.h
Examining data/squizz-0.99d+dfsg/lib/sequence/gdel.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gdey.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gdey.h
Examining data/squizz-0.99d+dfsg/lib/sequence/genbankl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/genbanky.c
Examining data/squizz-0.99d+dfsg/lib/sequence/genbanky.h
Examining data/squizz-0.99d+dfsg/lib/sequence/igl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/igy.c
Examining data/squizz-0.99d+dfsg/lib/sequence/igy.h
Examining data/squizz-0.99d+dfsg/lib/sequence/nbrfl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/nbrfy.c
Examining data/squizz-0.99d+dfsg/lib/sequence/nbrfy.h
Examining data/squizz-0.99d+dfsg/lib/sequence/rawl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/rawy.c
Examining data/squizz-0.99d+dfsg/lib/sequence/rawy.h
Examining data/squizz-0.99d+dfsg/lib/sequence/sprotl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/sproty.c
Examining data/squizz-0.99d+dfsg/lib/sequence/sproty.h
Examining data/squizz-0.99d+dfsg/lib/sequence/embl.c
Examining data/squizz-0.99d+dfsg/lib/sequence/fasta.c
Examining data/squizz-0.99d+dfsg/lib/sequence/genbank.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gcg.c
Examining data/squizz-0.99d+dfsg/lib/sequence/gde.c
Examining data/squizz-0.99d+dfsg/lib/sequence/ig.c
Examining data/squizz-0.99d+dfsg/lib/sequence/nbrf.c
Examining data/squizz-0.99d+dfsg/lib/sequence/codata.c
Examining data/squizz-0.99d+dfsg/lib/sequence/raw.c
Examining data/squizz-0.99d+dfsg/lib/sequence/sprot.c
Examining data/squizz-0.99d+dfsg/lib/sequence/parse.c
Examining data/squizz-0.99d+dfsg/lib/sequence/protein.c
Examining data/squizz-0.99d+dfsg/lib/sequence/utils.c
Examining data/squizz-0.99d+dfsg/lib/sequence.h
Examining data/squizz-0.99d+dfsg/lib/align.h
Examining data/squizz-0.99d+dfsg/lib/align.c
Examining data/squizz-0.99d+dfsg/lib/sequence.c
Examining data/squizz-0.99d+dfsg/lib/compat.h
Examining data/squizz-0.99d+dfsg/src/format.h
Examining data/squizz-0.99d+dfsg/src/squizz.c
Examining data/squizz-0.99d+dfsg/src/format.c
FINAL RESULTS:
data/squizz-0.99d+dfsg/lib/align/clustaly.c:630:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/megay.c:660:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/msf.c:73:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
(void)fprintf(f, " %s MSF: %"PRIsiz, q, len);
data/squizz-0.99d+dfsg/lib/align/msf.c:90:11: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
(void)fprintf(f, " Len: %5"PRIsiz, len);
data/squizz-0.99d+dfsg/lib/align/msfy.c:639:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/nexusiy.c:657:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/phylipiy.c:614:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/phylipsy.c:616:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align/stocky.c:619:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/compat/err.h:16:11: [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, ap);
data/squizz-0.99d+dfsg/lib/compat/err.h:28:11: [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, ap);
data/squizz-0.99d+dfsg/lib/compat/err.h:42:11: [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, ap);
data/squizz-0.99d+dfsg/lib/compat/err.h:54:11: [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, ap);
data/squizz-0.99d+dfsg/lib/extern/file.c:28:7: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access(name, F_OK) != -1) {
data/squizz-0.99d+dfsg/lib/extern/file.c:38:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(void)sprintf(p, "%s/%s", q, name);
data/squizz-0.99d+dfsg/lib/extern/file.c:39:9: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access(p, F_OK) != -1) {
data/squizz-0.99d+dfsg/lib/extern/file.c:47:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(void)sprintf(p, "%s/%s", BIODATADIR, name);
data/squizz-0.99d+dfsg/lib/extern/file.c:48:7: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access(p, F_OK) != -1) {
data/squizz-0.99d+dfsg/lib/extern/text.c:36:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
if (strcat(dst, src) == NULL) {
data/squizz-0.99d+dfsg/lib/extern/text.c:69:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
if (strcat(dst, p) == NULL) {
data/squizz-0.99d+dfsg/lib/sequence/codata.c:92:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
(void)fprintf(f, "SUMMARY #length %"PRIsiz, seq->strlen);
data/squizz-0.99d+dfsg/lib/sequence/codatay.c:837:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/embly.c:912:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/fastay.c:612:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/gcgy.c:620:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/gdey.c:603:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/genbanky.c:995:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/igy.c:619:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/nbrfy.c:621:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/rawy.c:592:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/sequence/sproty.c:929:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define YYFPRINTF fprintf
data/squizz-0.99d+dfsg/lib/align.c:156:8: [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.
d = (getenv("SQUIZZ_DEBUG") != NULL) ? 1 : 0;
data/squizz-0.99d+dfsg/lib/align/parse.c:40:8: [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.
d = (getenv("SQUIZZ_DEBUG") != NULL) ? 1 : 0;
data/squizz-0.99d+dfsg/lib/extern/file.c:34:12: [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.
if ((q = getenv("BIODATADIR")) != NULL) {
data/squizz-0.99d+dfsg/lib/sequence.c:148:8: [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.
d = (getenv("SQUIZZ_DEBUG") != NULL) ? 1 : 0;
data/squizz-0.99d+dfsg/src/squizz.c:43:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((i = getopt(argc, argv, "ASc:f:hlnsv")) != -1) {
data/squizz-0.99d+dfsg/lib/align/clustaly.c:877:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/clustaly.c:1086:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/megay.c:907:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/megay.c:1116:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/msf.c:50:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *p, *b, *e, *nam, c, d[255];
data/squizz-0.99d+dfsg/lib/align/msfy.c:886:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/msfy.c:1095:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/nexusiy.c:904:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/nexusiy.c:1113:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/phylipiy.c:861:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/phylipiy.c:1070:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/phylipsy.c:863:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/phylipsy.c:1072:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/align/stocky.c:866:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/align/stocky.c:1075:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/extern/text.c:18:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
return memcpy(nstr, str, nlen); }
data/squizz-0.99d+dfsg/lib/sequence/codatay.c:1084:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/codatay.c:1305:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/embll.c:7869:17: [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).
{ yylval->num = atoi(embltext); return SVNUM; }
data/squizz-0.99d+dfsg/lib/sequence/embly.c:1159:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/embly.c:1416:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/fastay.c:859:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/fastay.c:1074:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/gcg.c:47:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *p, c, d[255];
data/squizz-0.99d+dfsg/lib/sequence/gcgy.c:867:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/gcgy.c:1070:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/gdey.c:850:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/gdey.c:1059:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/genbankl.c:8671:17: [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).
{ yylval->num = atoi(genbanktext); return VENUM; }
data/squizz-0.99d+dfsg/lib/sequence/genbankl.c:8697:17: [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).
{ yylval->num = atoi(genbanktext); return GINUM; }
data/squizz-0.99d+dfsg/lib/sequence/genbanky.c:1242:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/genbanky.c:1481:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/igy.c:866:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/igy.c:1081:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/nbrfy.c:868:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/nbrfy.c:1083:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/rawy.c:839:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/rawy.c:1042:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/lib/sequence/sproty.c:1176:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/squizz-0.99d+dfsg/lib/sequence/sproty.c:1421:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char yymsgbuf[128];
data/squizz-0.99d+dfsg/src/squizz.c:29:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *file, *prg, buf[1024];
data/squizz-0.99d+dfsg/src/squizz.c:99:12: [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).
if ((f = fopen(file, "r")) == NULL) {
data/squizz-0.99d+dfsg/lib/align.c:166:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = ali->seq; n = 0; len = (*p)->strlen;
data/squizz-0.99d+dfsg/lib/align.c:168:15: [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 ((*p)->strlen != len) { n++; }
data/squizz-0.99d+dfsg/lib/align/clustal.c:49:29: [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).
s = ali->seq; len = (*s)->strlen;
data/squizz-0.99d+dfsg/lib/align/clustal.c:56:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen((*s)->nam) > 15) {
data/squizz-0.99d+dfsg/lib/align/clustal.c:117:29: [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).
s = ali->seq; len = (*s)->strlen;
data/squizz-0.99d+dfsg/lib/align/clustall.c:1359:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( clustalin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/clustall.c:2411:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return clustal_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/clustaly.c:777:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/megal.c:2424:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( megain )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/megal.c:3619:31: [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).
return mega_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/megay.c:807:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/msf.c:63:15: [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).
len = (*s)->strlen;
data/squizz-0.99d+dfsg/lib/align/msf.c:81:9: [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).
l = strlen((*s)->nam);
data/squizz-0.99d+dfsg/lib/align/msf.c:113:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = sequence_fixnam((*s)->nam); l = strlen(p); j = nlen;
data/squizz-0.99d+dfsg/lib/align/msfl.c:4813:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( msfin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/msfl.c:5886:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return msf_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/msfy.c:786:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/nexusi.c:52:29: [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).
s = ali->seq; len = (*s)->strlen;
data/squizz-0.99d+dfsg/lib/align/nexusil.c:5341:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( nexusiin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/nexusil.c:6552:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return nexusi_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/nexusiy.c:804:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/phylip.c:24:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(new) > 10) {
data/squizz-0.99d+dfsg/lib/align/phylipi.c:51:29: [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).
s = ali->seq; len = (*s)->strlen; n = 0;
data/squizz-0.99d+dfsg/lib/align/phylipil.c:779:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( phylipiin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/phylipil.c:1809:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return phylipi_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/phylipiy.c:761:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/phylips.c:50:29: [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).
s = ali->seq; len = (*s)->strlen; n = 0;
data/squizz-0.99d+dfsg/lib/align/phylipsl.c:758:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( phylipsin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/phylipsl.c:1786:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return phylips_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/phylipsy.c:763:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/align/stock.c:53:11: [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).
len = strlen((*s)->nam);
data/squizz-0.99d+dfsg/lib/align/stock.c:62:29: [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).
s = ali->seq; len = (*s)->strlen;
data/squizz-0.99d+dfsg/lib/align/stockl.c:892:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( stockin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/align/stockl.c:1921:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return stock_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/align/stocky.c:766:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/extern/file.c:31:17: [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).
p = NULL; l = strlen(name);
data/squizz-0.99d+dfsg/lib/extern/file.c:35:11: [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).
len = strlen(q) + 1 + l;
data/squizz-0.99d+dfsg/lib/extern/file.c:44:9: [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(BIODATADIR) + 1 + l;
data/squizz-0.99d+dfsg/lib/extern/text.c:28:9: [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(src);
data/squizz-0.99d+dfsg/lib/extern/text.c:29:29: [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).
if (dst != NULL) { len += strlen(dst); }
data/squizz-0.99d+dfsg/lib/extern/text.c:59:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = i + strlen(p);
data/squizz-0.99d+dfsg/lib/extern/text.c:60:29: [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).
if (dst != NULL) { len += strlen(dst); }
data/squizz-0.99d+dfsg/lib/extern/text.c:67:17: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
if (i == 1 && strcat(dst, " ") == NULL) {
data/squizz-0.99d+dfsg/lib/sequence.c:152:11: [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).
seq->strlen); }
data/squizz-0.99d+dfsg/lib/sequence.c:227:9: [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(seq);
data/squizz-0.99d+dfsg/lib/sequence.h:14:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t strlen;
data/squizz-0.99d+dfsg/lib/sequence/codata.c:83:11: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/codata.c:83:29: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/codata.c:92:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(void)fprintf(f, "SUMMARY #length %"PRIsiz, seq->strlen);
data/squizz-0.99d+dfsg/lib/sequence/codatal.c:6465:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( codatain )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/codatal.c:8059:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return codata_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/codatay.c:984:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/embl.c:56:25: [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).
t = "XXX"; len = seq->strlen;
data/squizz-0.99d+dfsg/lib/sequence/embl.c:68:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/embl.c:68:31: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/embl.c:110:11: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/embl.c:110:29: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/embl.c:153:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(void)fprintf(f, "SQ Sequence %"PRIsiz" BP", seq->strlen);
data/squizz-0.99d+dfsg/lib/sequence/embl.c:159:28: [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).
p = seq->str; len = seq->strlen;
data/squizz-0.99d+dfsg/lib/sequence/embll.c:7539:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( emblin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/embll.c:9376:31: [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).
return embl_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/embly.c:1059:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/fastal.c:1160:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( fastain )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/fastal.c:2158:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return fasta_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/fastay.c:759:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/gcg.c:68:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(void)fprintf(f, "%s Length: %"PRIsiz" %s", q, seq->strlen, d);
data/squizz-0.99d+dfsg/lib/sequence/gcgl.c:1144:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( gcgin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/gcgl.c:2162:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return gcg_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/gcgy.c:767:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/gdel.c:738:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( gdein )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/gdel.c:1724:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return gde_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/gdey.c:750:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/genbank.c:61:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(void)fprintf(f, "LOCUS %-16.16s %11"PRIsiz" bp", u, seq->strlen);
data/squizz-0.99d+dfsg/lib/sequence/genbank.c:102:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(*x);
data/squizz-0.99d+dfsg/lib/sequence/genbank.c:108:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
l += strlen(r) + len;
data/squizz-0.99d+dfsg/lib/sequence/genbank.c:129:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/genbankl.c:8235:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( genbankin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/genbankl.c:10296:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return genbank_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/genbanky.c:1142:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/igl.c:970:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( igin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/igl.c:2001:29: [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).
return ig_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/igy.c:766:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/nbrfl.c:942:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( nbrfin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/nbrfl.c:1981:31: [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).
return nbrf_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/nbrfy.c:768:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/parse.c:141:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t len = seq->strlen + strlen(str);
data/squizz-0.99d+dfsg/lib/sequence/parse.c:144:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p = str; q = seq->str + seq->strlen;
data/squizz-0.99d+dfsg/lib/sequence/rawl.c:681:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( rawin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/rawl.c:1597:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return raw_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/rawy.c:739:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:74:31: [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).
s = "Reviewed;"; len = seq->strlen;
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:86:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:86:31: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:132:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:132:31: [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).
len = strlen(*x); sep = strlen(s);
data/squizz-0.99d+dfsg/lib/sequence/sprot.c:162:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = seq->strlen; w = protein_weight(seq->str) + 0.5;
data/squizz-0.99d+dfsg/lib/sequence/sprotl.c:7305:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( sprotin )) != EOF && c != '\n'; ++n ) \
data/squizz-0.99d+dfsg/lib/sequence/sprotl.c:9261:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return sprot_scan_bytes(yystr,strlen(yystr) );
data/squizz-0.99d+dfsg/lib/sequence/sproty.c:1076:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
# define yystrlen strlen
ANALYSIS SUMMARY:
Hits = 177
Lines analyzed = 111268 in approximately 4.02 seconds (27665 lines/second)
Physical Source Lines of Code (SLOC) = 83717
Hits@level = [0] 171 [1] 99 [2] 42 [3] 5 [4] 31 [5] 0
Hits@level+ = [0+] 348 [1+] 177 [2+] 78 [3+] 36 [4+] 31 [5+] 0
Hits/KSLOC@level+ = [0+] 4.15686 [1+] 2.11427 [2+] 0.93171 [3+] 0.43002 [4+] 0.370295 [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.