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/minimap-0.2/bseq.c
Examining data/minimap-0.2/bseq.h
Examining data/minimap-0.2/example.c
Examining data/minimap-0.2/index.c
Examining data/minimap-0.2/khash.h
Examining data/minimap-0.2/kseq.h
Examining data/minimap-0.2/ksort.h
Examining data/minimap-0.2/kthread.c
Examining data/minimap-0.2/kvec.h
Examining data/minimap-0.2/main.c
Examining data/minimap-0.2/map.c
Examining data/minimap-0.2/minimap.h
Examining data/minimap-0.2/misc.c
Examining data/minimap-0.2/sdust.c
Examining data/minimap-0.2/sdust.h
Examining data/minimap-0.2/sketch.c
Examining data/minimap-0.2/kdq.h
FINAL RESULTS:
data/minimap-0.2/main.c:36:14: [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 ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lRPST:m:L:Dx:")) >= 0) {
data/minimap-0.2/sdust.c:187:14: [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 ((c = getopt(argc, argv, "w:t:")) >= 0) {
data/minimap-0.2/bseq.c:10:17: [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 unsigned char seq_nt4_table[256];
data/minimap-0.2/index.c:309:2: [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 magic[4];
data/minimap-0.2/kseq.h:127:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/minimap-0.2/kvec.h:74:3: [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((v1).a, (v0).a, sizeof(type) * (v0).n); \
data/minimap-0.2/main.c:37:21: [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 (c == 'w') w = atoi(optarg);
data/minimap-0.2/main.c:38:26: [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).
else if (c == 'k') k = atoi(optarg);
data/minimap-0.2/main.c:39:26: [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).
else if (c == 'b') b = atoi(optarg);
data/minimap-0.2/main.c:40:35: [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).
else if (c == 'r') opt.radius = atoi(optarg);
data/minimap-0.2/main.c:41:36: [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).
else if (c == 'c') opt.min_cnt = atoi(optarg);
data/minimap-0.2/main.c:44:34: [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).
else if (c == 't') n_threads = atoi(optarg);
data/minimap-0.2/main.c:45:35: [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).
else if (c == 'v') mm_verbose = atoi(optarg);
data/minimap-0.2/main.c:46:36: [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).
else if (c == 'g') opt.max_gap = atoi(optarg);
data/minimap-0.2/main.c:55:40: [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).
else if (c == 'T') opt.sdust_thres = atoi(optarg);
data/minimap-0.2/main.c:56:38: [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).
else if (c == 'L') opt.min_match = atoi(optarg);
data/minimap-0.2/main.c:115:20: [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 (is_idx) fpr = fopen(argv[optind], "rb");
data/minimap-0.2/main.c:117:17: [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 (fnw) fpw = fopen(fnw, "wb");
data/minimap-0.2/map.c:312:3: [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(step->reg[i], regs, n_regs * sizeof(mm_reg1_t));
data/minimap-0.2/sdust.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.
unsigned char seq_nt4_table[256] = {
data/minimap-0.2/sdust.c:42:17: [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 unsigned char seq_nt4_table[256];
data/minimap-0.2/sdust.c:108:2: [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, cv, SD_WTOT * sizeof(int));
data/minimap-0.2/sdust.c:188:21: [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 (c == 'w') W = atoi(optarg);
data/minimap-0.2/sdust.c:189:26: [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).
else if (c == 't') T = atoi(optarg);
data/minimap-0.2/sketch.c:8:10: [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.
unsigned char seq_nt4_table[256] = {
data/minimap-0.2/index.c:205:13: [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).
assert(strlen(s->seq[i].name) <= 254);
data/minimap-0.2/index.c:283:8: [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).
l = strlen(mi->name[i]);
data/minimap-0.2/sdust.c:141:25: [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).
if (l_seq < 0) l_seq = strlen((const char*)seq);
ANALYSIS SUMMARY:
Hits = 28
Lines analyzed = 2882 in approximately 0.11 seconds (26688 lines/second)
Physical Source Lines of Code (SLOC) = 2148
Hits@level = [0] 51 [1] 3 [2] 23 [3] 2 [4] 0 [5] 0
Hits@level+ = [0+] 79 [1+] 28 [2+] 25 [3+] 2 [4+] 0 [5+] 0
Hits/KSLOC@level+ = [0+] 36.7784 [1+] 13.0354 [2+] 11.6387 [3+] 0.931099 [4+] 0 [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.