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/seer-1.1.4/src/combineCmdLine.cpp
Examining data/seer-1.1.4/src/combineInit.cpp
Examining data/seer-1.1.4/src/combineKmers.cpp
Examining data/seer-1.1.4/src/combineKmers.hpp
Examining data/seer-1.1.4/src/covar.cpp
Examining data/seer-1.1.4/src/covar.hpp
Examining data/seer-1.1.4/src/fasta.cpp
Examining data/seer-1.1.4/src/fasta.hpp
Examining data/seer-1.1.4/src/filterCmdLine.cpp
Examining data/seer-1.1.4/src/filter_seer.cpp
Examining data/seer-1.1.4/src/filter_seer.hpp
Examining data/seer-1.1.4/src/kmds.hpp
Examining data/seer-1.1.4/src/kmdsCmdLine.cpp
Examining data/seer-1.1.4/src/kmdsMain.cpp
Examining data/seer-1.1.4/src/kmdsStruct.cpp
Examining data/seer-1.1.4/src/kmer.cpp
Examining data/seer-1.1.4/src/kmer.hpp
Examining data/seer-1.1.4/src/linearFunction.cpp
Examining data/seer-1.1.4/src/linkFunction.hpp
Examining data/seer-1.1.4/src/logitFunction.cpp
Examining data/seer-1.1.4/src/mapCmdLine.cpp
Examining data/seer-1.1.4/src/mapMain.cpp
Examining data/seer-1.1.4/src/map_back.hpp
Examining data/seer-1.1.4/src/sample.cpp
Examining data/seer-1.1.4/src/sample.hpp
Examining data/seer-1.1.4/src/seer.hpp
Examining data/seer-1.1.4/src/seerBasicFilter.cpp
Examining data/seer-1.1.4/src/seerBinaryAssoc.cpp
Examining data/seer-1.1.4/src/seerCmdLine.cpp
Examining data/seer-1.1.4/src/seerCommon.cpp
Examining data/seer-1.1.4/src/seerContinuousAssoc.cpp
Examining data/seer-1.1.4/src/seerErr.cpp
Examining data/seer-1.1.4/src/seerIO.cpp
Examining data/seer-1.1.4/src/seerMain.cpp
Examining data/seer-1.1.4/src/seerStats.cpp
Examining data/seer-1.1.4/src/seercommon.hpp
Examining data/seer-1.1.4/src/significant_kmer.cpp
Examining data/seer-1.1.4/src/significant_kmer.hpp

FINAL RESULTS:

data/seer-1.1.4/src/kmdsMain.cpp:108:24:  [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).
         filtered_file.open(output_file_name.c_str());
data/seer-1.1.4/src/seerIO.cpp:61:15:  [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).
   dsm_stream.open(file_name.c_str()); // Push binary file into buffer

ANALYSIS SUMMARY:

Hits = 2
Lines analyzed = 4364 in approximately 0.17 seconds (26006 lines/second)
Physical Source Lines of Code (SLOC) = 2944
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+] 0.679348 [1+] 0.679348 [2+] 0.679348 [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.