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/filtlong-0.2.0/src/args.h
Examining data/filtlong-0.2.0/src/arguments.cpp
Examining data/filtlong-0.2.0/src/arguments.h
Examining data/filtlong-0.2.0/src/bloom_filter.h
Examining data/filtlong-0.2.0/src/kmers.cpp
Examining data/filtlong-0.2.0/src/kmers.h
Examining data/filtlong-0.2.0/src/kseq.h
Examining data/filtlong-0.2.0/src/main.cpp
Examining data/filtlong-0.2.0/src/misc.cpp
Examining data/filtlong-0.2.0/src/misc.h
Examining data/filtlong-0.2.0/src/read.cpp
Examining data/filtlong-0.2.0/src/read.h

FINAL RESULTS:

data/filtlong-0.2.0/src/bloom_filter.h:534:10:  [3] (random) srand:
  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.
         srand(static_cast<unsigned int>(random_seed_));
data/filtlong-0.2.0/src/bloom_filter.h:34:23:  [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 bit_mask[bits_per_char] = {
data/filtlong-0.2.0/src/kseq.h:129:4:  [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/filtlong-0.2.0/src/main.cpp:104:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            reads.push_back(read);
data/filtlong-0.2.0/src/main.cpp:112:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            read_dict[read->m_name] = read;
data/filtlong-0.2.0/src/main.cpp:138:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads) {
data/filtlong-0.2.0/src/main.cpp:140:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            reads2.push_back(read);
data/filtlong-0.2.0/src/main.cpp:148:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:156:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        for (auto read : reads2)
data/filtlong-0.2.0/src/main.cpp:172:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:181:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:201:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:222:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:251:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            for (auto read : reads2) {
data/filtlong-0.2.0/src/main.cpp:315:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto read : reads)
data/filtlong-0.2.0/src/main.cpp:316:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        delete read;

ANALYSIS SUMMARY:

Hits = 16
Lines analyzed = 4698 in approximately 0.14 seconds (34548 lines/second)
Physical Source Lines of Code (SLOC) = 3442
Hits@level = [0]   0 [1]  13 [2]   2 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]  16 [1+]  16 [2+]   3 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 4.64846 [1+] 4.64846 [2+] 0.871586 [3+] 0.290529 [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.