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.