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/physamp-1.1.0/physamp/AlignmentOptimizer.cpp
Examining data/physamp-1.1.0/physamp/PhyloSampler.cpp

FINAL RESULTS:

data/physamp-1.1.0/physamp/PhyloSampler.cpp:122:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    dist.reset(matIO.read(distPath));

ANALYSIS SUMMARY:

Hits = 1
Lines analyzed = 1043 in approximately 0.04 seconds (25281 lines/second)
Physical Source Lines of Code (SLOC) = 793
Hits@level = [0]   0 [1]   1 [2]   0 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   1 [1+]   1 [2+]   0 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 1.26103 [1+] 1.26103 [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.