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/axe-demultiplexer-0.3.3+dfsg/src/axe.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/alpha-map-private.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/alpha-map.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/alpha-map.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/darray.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/darray.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring-private.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/tail.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/tail.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie-private.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie-string.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie-string.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/triedefs.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/datrie/typedefs.h
Examining data/axe-demultiplexer-0.3.3+dfsg/src/main.c
Examining data/axe-demultiplexer-0.3.3+dfsg/src/axe.c
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/test.c
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/test_libaxe.c
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/tests.h
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.h
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_demo.c
Examining data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_macros.h

FINAL RESULTS:

data/axe-demultiplexer-0.3.3+dfsg/tests/test.c:52:9:  [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(data_prefix, W_OK | X_OK | R_OK) != 0) {
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_macros.h:44:2:  [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.
	printf args ;						\
data/axe-demultiplexer-0.3.3+dfsg/src/main.c:139:17:  [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.
    while ((c = getopt_long(argc, argv, axe_opts, axe_longopts, &optind)) > 0){
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:33:1:  [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 _time_now[10] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:172:5:  [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 buf[4096];
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:253:5:  [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 seq1[100] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:254:5:  [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 seq2[100] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:255:5:  [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 id[100] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:292:5:  [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 seq[100] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:293:5:  [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 id[100] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:564:9:  [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 tmp[3] = "";
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:1562:14:  [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).
    tab_fp = fopen(config->table_file, "w");
data/axe-demultiplexer-0.3.3+dfsg/src/axe.h:86:5:  [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 *infiles[2];
data/axe-demultiplexer-0.3.3+dfsg/src/axe.h:87:5:  [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 *out_prefixes[2];
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.c:109:5:  [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 (dst->val, src->val, (src->str_len + 1) * src->char_size);
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.c:129:5:  [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 ((char *)dst->val + (dst->char_size * dst->str_len), src->val,
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.c:143:5:  [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 ((char  *)ds->val + (ds->char_size * ds->str_len), data,
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/dstring.c:157:5:  [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 ((char *)ds->val + (ds->char_size * ds->str_len), data,
data/axe-demultiplexer-0.3.3+dfsg/src/main.c:142:38:  [2] (integer) atol:
  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).
                config->mismatches = atol(optarg);
data/axe-demultiplexer-0.3.3+dfsg/src/main.c:145:46:  [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).
                config->out_compress_level = atoi(optarg);
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:84:8:  [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 char commandname[MAX_PATH+1];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:134:2:  [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 buffer[LONGEST_TEST_NAME+256];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:187:3:  [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 b[1];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:202:3:  [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 b[1];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:282:2:  [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 fullname[LONGEST_TEST_NAME];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_demo.c:106:2:  [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 buffer1[512];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_demo.c:107:2:  [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 buffer2[512];
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_demo.c:154:2:  [2] (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). Risk is low because the source is a constant string.
	strcpy(db->buffer1, "String 0");
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest_demo.c:155:2:  [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(db->buffer2, db->buffer1, sizeof(db->buffer1));
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:169:67:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
_axe_format_outfile_path (const char *prefix, const char *id, int read,
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:182:18:  [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).
    prefix_len = strlen(prefix);
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:190:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(our_prefix, prefix, prefix_len);
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:194:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read > 0) {
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:195:66:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        res = snprintf(buf, 4096, "%s%s_R%d.%s", our_prefix, id, read, ext);
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:262:11:  [1] (buffer) sscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
    res = sscanf(line, "%99s\t%99s\t%99s", seq1, seq2, id);
data/axe-demultiplexer-0.3.3+dfsg/src/axe.c:300:11:  [1] (buffer) sscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
    res = sscanf(line, "%99s\t%99s", seq, id);
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/alpha-map.c:362:40:  [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).
    alpha_str = (AlphaChar *) malloc ((strlen ((const char *)str) + 1)
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie-string.c:91:40:  [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).
                                  str, strlen ((const char *)str));
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie.c:888:46:  [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).
                                          * (strlen ((const char *)tail_str)
data/axe-demultiplexer-0.3.3+dfsg/src/datrie/trie.c:905:38:  [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).
                        * (key_len + strlen ((const char *)tail_str) + 1)
data/axe-demultiplexer-0.3.3+dfsg/tests/test_libaxe.c:72:48:  [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).
    mutated  = hamming_mutate_dna(&count, str, strlen(str), 2, 1);
data/axe-demultiplexer-0.3.3+dfsg/tests/tinytest/tinytest.c:206:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		r = (int)read(outcome_pipe[0], b, 1);

ANALYSIS SUMMARY:

Hits = 42
Lines analyzed = 7298 in approximately 0.21 seconds (34601 lines/second)
Physical Source Lines of Code (SLOC) = 4480
Hits@level = [0] 126 [1]  13 [2]  26 [3]   1 [4]   2 [5]   0
Hits@level+ = [0+] 168 [1+]  42 [2+]  29 [3+]   3 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 37.5 [1+] 9.375 [2+] 6.47321 [3+] 0.669643 [4+] 0.446429 [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.