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/amap-align-2.2+git20080214.600fc29+dfsg/align/Defaults.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/EvolutionaryTree.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/FileBuffer.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/MultiSequence.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/ProbabilisticModel.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/ScoreType.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/Sequence.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/SparseMatrix.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/MultiSequenceDag.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/SafeVector.h
Examining data/amap-align-2.2+git20080214.600fc29+dfsg/align/Amap.cc

FINAL RESULTS:

data/amap-align-2.2+git20080214.600fc29+dfsg/align/Sequence.h:154:5:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    sscanf (header.c_str(), "%s", name);
data/amap-align-2.2+git20080214.600fc29+dfsg/align/Amap.cc:316:18:  [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).
    FILE *file = fopen (filename, "w");
data/amap-align-2.2+git20080214.600fc29+dfsg/align/Amap.cc:1120:10:  [2] (misc) open:
  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).
    data.open (parametersInputFilename.c_str());
data/amap-align-2.2+git20080214.600fc29+dfsg/align/FileBuffer.h:27:3:  [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 buffer[BufferSize];
data/amap-align-2.2+git20080214.600fc29+dfsg/align/MultiSequenceDag.h:379:16:  [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 char pepGroup[26];             // peptide groups for GUI coloring (from TEXshade)
data/amap-align-2.2+git20080214.600fc29+dfsg/align/Sequence.h:153:5:  [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 name[1024];
data/amap-align-2.2+git20080214.600fc29+dfsg/align/FileBuffer.h:58:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      file.read (buffer, BufferSize);

ANALYSIS SUMMARY:

Hits = 7
Lines analyzed = 5845 in approximately 0.17 seconds (34479 lines/second)
Physical Source Lines of Code (SLOC) = 3482
Hits@level = [0]  11 [1]   1 [2]   5 [3]   0 [4]   1 [5]   0
Hits@level+ = [0+]  18 [1+]   7 [2+]   6 [3+]   1 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 5.16944 [1+] 2.01034 [2+] 1.72315 [3+] 0.287191 [4+] 0.287191 [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.