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/sickle-1.33+git20150314.f3d6ae3/src/kseq.h
Examining data/sickle-1.33+git20150314.f3d6ae3/src/print_record.c
Examining data/sickle-1.33+git20150314.f3d6ae3/src/print_record.h
Examining data/sickle-1.33+git20150314.f3d6ae3/src/sickle.c
Examining data/sickle-1.33+git20150314.f3d6ae3/src/sickle.h
Examining data/sickle-1.33+git20150314.f3d6ae3/src/sliding.c
Examining data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c
Examining data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c
FINAL RESULTS:
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:135:13: [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(infn1, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:140:13: [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(infn2, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:145:13: [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(infnc, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:160:13: [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(outfn1, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:165:13: [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(outfn2, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:170:13: [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(outfnc, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:176:13: [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(outfnc, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:182:13: [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(sfn, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:90:13: [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(infn, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:108:13: [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(outfn, optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:124:16: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
optc = getopt_long(argc, argv, "df:r:c:t:o:p:m:M:s:q:l:xng", paired_long_options, &option_index);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:79:16: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
optc = getopt_long(argc, argv, "df:t:o:q:l:zxng", single_long_options, &option_index);
data/sickle-1.33+git20150314.f3d6ae3/src/kseq.h:123:16: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/sickle-1.33+git20150314.f3d6ae3/src/sickle.h:71:14: [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 typenames[4][10] = {
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:186:37: [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).
paired_qual_threshold = atoi(optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:194:39: [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).
paired_length_threshold = atoi(optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:266:21: [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).
combo = fopen(outfnc, "w");
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:316:24: [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).
outfile1 = fopen(outfn1, "w");
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:322:24: [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).
outfile2 = fopen(outfn2, "w");
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:346:22: [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).
single = fopen(sfn, "w");
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:112:37: [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).
single_qual_threshold = atoi(optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:120:39: [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).
single_length_threshold = atoi(optarg);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:177:19: [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(outfn, "w");
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:134:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
infn1 = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:139:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
infn2 = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:144:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
infnc = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:159:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outfn1 = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:164:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outfn2 = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:169:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outfnc = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:175:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outfnc = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_paired.c:181:35: [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).
sfn = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:89:36: [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).
infn = (char *) malloc(strlen(optarg) + 1);
data/sickle-1.33+git20150314.f3d6ae3/src/trim_single.c:107:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outfn = (char *) malloc(strlen(optarg) + 1);
ANALYSIS SUMMARY:
Hits = 33
Lines analyzed = 1325 in approximately 0.06 seconds (22958 lines/second)
Physical Source Lines of Code (SLOC) = 1002
Hits@level = [0] 74 [1] 10 [2] 11 [3] 2 [4] 10 [5] 0
Hits@level+ = [0+] 107 [1+] 33 [2+] 23 [3+] 12 [4+] 10 [5+] 0
Hits/KSLOC@level+ = [0+] 106.786 [1+] 32.9341 [2+] 22.9541 [3+] 11.976 [4+] 9.98004 [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.