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/scythe-0.994+git20141017.20d3cff/src/kseq.h
Examining data/scythe-0.994+git20141017.20d3cff/src/match.c
Examining data/scythe-0.994+git20141017.20d3cff/src/scythe.h
Examining data/scythe-0.994+git20141017.20d3cff/src/tests/tests.c
Examining data/scythe-0.994+git20141017.20d3cff/src/util.c
Examining data/scythe-0.994+git20141017.20d3cff/src/prob.c
Examining data/scythe-0.994+git20141017.20d3cff/src/scythe.c

FINAL RESULTS:

data/scythe-0.994+git20141017.20d3cff/src/prob.c:75:21:  [3] (random) random:
  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.
  ps->random = (ls->random * (1-p_prior))/p_denom;
data/scythe-0.994+git20141017.20d3cff/src/prob.c:76:36:  [3] (random) random:
  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.
  ps->is_contam = ps->contam > ps->random;
data/scythe-0.994+git20141017.20d3cff/src/prob.c:92:11:  [3] (random) random:
  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.
      ls->random *= p_match; /* prob match happened by chance */
data/scythe-0.994+git20141017.20d3cff/src/prob.c:96:11:  [3] (random) random:
  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.
      ls->random *= 1 - p_match;
data/scythe-0.994+git20141017.20d3cff/src/scythe.c:130:12:  [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, "dtfp:a:o:q:m:o:n:M:", long_options, &option_index);
data/scythe-0.994+git20141017.20d3cff/src/scythe.h:67:10:  [3] (random) random:
  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.
  double random;
data/scythe-0.994+git20141017.20d3cff/src/scythe.h:73:10:  [3] (random) random:
  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.
  double random;
data/scythe-0.994+git20141017.20d3cff/src/util.c:229:41:  [3] (random) random:
  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.
          match->ps->contam, match->ps->random,
data/scythe-0.994+git20141017.20d3cff/src/kseq.h:125:4:  [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/scythe-0.994+git20141017.20d3cff/src/scythe.c:154:21:  [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).
        output_fp = fopen(optarg, "w");
data/scythe-0.994+git20141017.20d3cff/src/scythe.c:161:22:  [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).
        matches_fp = fopen(optarg, "w");
data/scythe-0.994+git20141017.20d3cff/src/scythe.c:168:15:  [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 = atoi(optarg);
data/scythe-0.994+git20141017.20d3cff/src/scythe.c:171:20:  [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).
        min_keep = atoi(optarg);
data/scythe-0.994+git20141017.20d3cff/src/util.c:93:3:  [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(out, "%.*s\n", n, seqa);
data/scythe-0.994+git20141017.20d3cff/src/util.c:103:3:  [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(ptr, "\n%.*s", (int) n, seqb);
data/scythe-0.994+git20141017.20d3cff/src/match.c:38:61:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
match *find_best_match(const adapter_array *aa, const char *read,
data/scythe-0.994+git20141017.20d3cff/src/match.c:50:19:  [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 al, rl = strlen(read);
data/scythe-0.994+git20141017.20d3cff/src/match.c:50:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_t al, rl = strlen(read);
data/scythe-0.994+git20141017.20d3cff/src/match.c:65:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      score_sequence(curr_arr, &(read)[shift], (aa->adapters[i]).seq, al);
data/scythe-0.994+git20141017.20d3cff/src/prob.c:26:14:  [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).
  int i, n = strlen(qual), q;
data/scythe-0.994+git20141017.20d3cff/src/tests/tests.c:38:38:  [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).
  score_sequence(cmp1_t, seqa, seqb, strlen(seqa));
data/scythe-0.994+git20141017.20d3cff/src/tests/tests.c:43:47:  [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).
  TEST(sum(score_sequence(cmp1_t, seqa, seqb, strlen(seqa)), strlen(seqa)) == 22, "sum of score_sequence");
data/scythe-0.994+git20141017.20d3cff/src/tests/tests.c:43:62:  [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).
  TEST(sum(score_sequence(cmp1_t, seqa, seqb, strlen(seqa)), strlen(seqa)) == 22, "sum of score_sequence");
data/scythe-0.994+git20141017.20d3cff/src/util.c:48:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(adapters[i].seq, aseq->seq.s, seq_l);
data/scythe-0.994+git20141017.20d3cff/src/util.c:51:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(adapters[i].name, aseq->name.s, aseq->name.l+1);
data/scythe-0.994+git20141017.20d3cff/src/util.c:54:7:  [1] (buffer) strncat:
  Easily used incorrectly (e.g., incorrectly computing the correct maximum
  size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
  or automatically resizing strings. Risk is low because the source is a
  constant character.
      strncat(adapters[i].name, " ", 1);
data/scythe-0.994+git20141017.20d3cff/src/util.c:55:7:  [1] (buffer) strncat:
  Easily used incorrectly (e.g., incorrectly computing the correct maximum
  size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
  or automatically resizing strings.
      strncat(adapters[i].name, aseq->comment.s, aseq->comment.l+1);
data/scythe-0.994+git20141017.20d3cff/src/util.c:97:7:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
      sprintf(ptr, "|");
data/scythe-0.994+git20141017.20d3cff/src/util.c:99:7:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
      sprintf(ptr, " ");

ANALYSIS SUMMARY:

Hits = 29
Lines analyzed = 1128 in approximately 0.05 seconds (22806 lines/second)
Physical Source Lines of Code (SLOC) = 845
Hits@level = [0]  42 [1]  14 [2]   7 [3]   8 [4]   0 [5]   0
Hits@level+ = [0+]  71 [1+]  29 [2+]  15 [3+]   8 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 84.0237 [1+] 34.3195 [2+] 17.7515 [3+] 9.46746 [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.