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/transrate-tools-1.0.0/src/bam-read.cpp
Examining data/transrate-tools-1.0.0/src/pileup.cpp
Examining data/transrate-tools-1.0.0/src/segmenter.cpp
Examining data/transrate-tools-1.0.0/src/segmenter.h
Examining data/transrate-tools-1.0.0/src/bam-read.h
Examining data/transrate-tools-1.0.0/src/pileup.h

FINAL RESULTS:

data/transrate-tools-1.0.0/src/bam-read.cpp:92:13:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      len = atoi(it[i].Length.c_str());
data/transrate-tools-1.0.0/src/bam-read.cpp:197:12:  [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).
    output.open (argv[2]);

ANALYSIS SUMMARY:

Hits = 2
Lines analyzed = 591 in approximately 0.02 seconds (27301 lines/second)
Physical Source Lines of Code (SLOC) = 449
Hits@level = [0]   0 [1]   0 [2]   2 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   2 [1+]   2 [2+]   2 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 4.45434 [1+] 4.45434 [2+] 4.45434 [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.