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/pizzly-0.37.3+ds/FilterFusions.hpp
Examining data/pizzly-0.37.3+ds/GeneModel.hpp
Examining data/pizzly-0.37.3+ds/common.h
Examining data/pizzly-0.37.3+ds/main.cpp

FINAL RESULTS:

data/pizzly-0.37.3+ds/FilterFusions.hpp:335:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      seqan::CharString read(seq.c_str());
data/pizzly-0.37.3+ds/FilterFusions.hpp:338:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
data/pizzly-0.37.3+ds/FilterFusions.hpp:403:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        seqan::CharString read(seq.c_str());
data/pizzly-0.37.3+ds/FilterFusions.hpp:408:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        seqan::setSource(readRowLeft, read);
data/pizzly-0.37.3+ds/FilterFusions.hpp:409:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        seqan::setSource(readRowRight, read);

ANALYSIS SUMMARY:

Hits = 5
Lines analyzed = 1765 in approximately 0.30 seconds (5903 lines/second)
Physical Source Lines of Code (SLOC) = 1458
Hits@level = [0]   0 [1]   5 [2]   0 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   5 [1+]   5 [2+]   0 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 3.42936 [1+] 3.42936 [2+]   0 [3+]   0 [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.