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/sibsim4-0.20/align.c
Examining data/sibsim4-0.20/sim4b1.h
Examining data/sibsim4-0.20/align.h
Examining data/sibsim4-0.20/sim4.h
Examining data/sibsim4-0.20/sim4b1.c
Examining data/sibsim4-0.20/misc.c
Examining data/sibsim4-0.20/misc.h
Examining data/sibsim4-0.20/sim4.init.c
FINAL RESULTS:
data/sibsim4-0.20/misc.c:31:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, fmt, ap);
data/sibsim4-0.20/misc.h:16:30: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__ ((format (printf, 1, 2) , __noreturn__));
data/sibsim4-0.20/sim4.init.c:283:5: [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.
fprintf(stderr, Usage, argv[0],
data/sibsim4-0.20/sim4.init.c:151:13: [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.
int c = getopt(argc, argv, "A:C:c:E:f:g:H:I:K:L:M:o:q:R:r:S:s:W:X:");
data/sibsim4-0.20/misc.c:22:10: [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.
extern char dna_seq_head[256];
data/sibsim4-0.20/misc.c:23:10: [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.
extern char rna_seq_head[256];
data/sibsim4-0.20/sim4.h:64:3: [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 in[BUF_SIZE];
data/sibsim4-0.20/sim4.init.c:112:1: [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 dna_seq_head[256];
data/sibsim4-0.20/sim4.init.c:113:1: [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 rna_seq_head[256];
data/sibsim4-0.20/sim4.init.c:156:26: [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).
options.ali_flag = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:161:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:168:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:175:24: [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).
options.cutoff = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:180:42: [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).
options.filterPct = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:185:39: [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).
options.gapPct = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:190:44: [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).
options.huntChimera = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:195:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:202:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:234:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:241:17: [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).
int val = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:248:31: [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).
options.mismatchScore = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:251:40: [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).
options.reverse = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:256:28: [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).
options.matchScore = atoi(optarg);
data/sibsim4-0.20/sim4.init.c:259:44: [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).
options.spliceInDel = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:262:46: [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).
options.splitScorePct = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:267:34: [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).
options.W = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:272:34: [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).
options.X = (unsigned int) atoi(optarg);
data/sibsim4-0.20/sim4.init.c:444:23: [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 unsigned char dna_complement[256] =
data/sibsim4-0.20/sim4.init.c:521:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *pSig, buf[51];
data/sibsim4-0.20/sim4.init.c:551:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *pSig, buf[51];
data/sibsim4-0.20/sim4.init.c:705:14: [2] (misc) open:
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).
sp->fd = open(fName, O_RDONLY);
data/sibsim4-0.20/sim4.init.c:734:3: [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(sp->header, buf, (sp->rb.lc + 1) * sizeof(char));
data/sibsim4-0.20/sim4b1.c:1289:7: [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(c, mp, sizeof(exon_t));
data/sibsim4-0.20/sim4b1.c:2278:3: [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(eCol->e.elt + pos, aCol->e.elt, aCol->nb * sizeof(void *));
data/sibsim4-0.20/sim4b1.c:2392:3: [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(splice, seq1 + splS->to1, 2UL);
data/sibsim4-0.20/sim4b1.c:2393:3: [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(splice + 2, seq1 + splS->nFrom1 - 3, 2UL);
data/sibsim4-0.20/sim4b1.c:2440:3: [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(s + options.scoreSplice_window, jct, 4UL);
data/sibsim4-0.20/sim4b1.c:2447:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(s, seq2 + to2 - options.scoreSplice_window + j,
data/sibsim4-0.20/sim4b1.c:2449:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(s + options.scoreSplice_window + 4, seq2 + to2 + j,
data/sibsim4-0.20/sim4.init.c:210:20: [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).
size_t len = strlen(optarg);
data/sibsim4-0.20/sim4.init.c:310:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(dna_seq_head, seq1.header, 256UL);
data/sibsim4-0.20/sim4.init.c:327:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(rna_seq_head, seq2.header, 256UL);
data/sibsim4-0.20/sim4.init.c:539:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, (char *) s1->seq + e->to1 - scanLen, (size_t) scanLen);
data/sibsim4-0.20/sim4.init.c:568:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, (char *) s1->seq + e->from1 - 1, 50UL);
data/sibsim4-0.20/sim4.init.c:671:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((rc = read(fd, b->in + b->ic,
ANALYSIS SUMMARY:
Hits = 45
Lines analyzed = 4448 in approximately 0.14 seconds (32865 lines/second)
Physical Source Lines of Code (SLOC) = 3792
Hits@level = [0] 61 [1] 6 [2] 35 [3] 1 [4] 3 [5] 0
Hits@level+ = [0+] 106 [1+] 45 [2+] 39 [3+] 4 [4+] 3 [5+] 0
Hits/KSLOC@level+ = [0+] 27.9536 [1+] 11.8671 [2+] 10.2848 [3+] 1.05485 [4+] 0.791139 [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.