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/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp
Examining data/ariba-2.14.6+ds/ariba/ext/vcfcall_ariba.cpp
Examining data/ariba-2.14.6+ds/ariba/ext/fml-asm_ariba.cpp

FINAL RESULTS:

data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:86:9:  [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).
    ofs.open(readsOutfile.c_str());
data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:247:9:  [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).
    ifs.open(filename.c_str());
data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:292:9:  [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).
    ofs.open(outfile.c_str());
data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:311:9:  [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).
    ofs.open(outfile.c_str());
data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:335:9:  [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).
    ofs.open(outfile.c_str());
data/ariba-2.14.6+ds/ariba/ext/minimap_ariba.cpp:354:9:  [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).
    ofs.open(outfile.c_str());
data/ariba-2.14.6+ds/ariba/ext/vcfcall_ariba.cpp:68:9:  [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).
    ofs.open(filename.c_str());
data/ariba-2.14.6+ds/ariba/ext/vcfcall_ariba.cpp:205:9:  [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).
    ifs.open(infile.c_str());

ANALYSIS SUMMARY:

Hits = 8
Lines analyzed = 899 in approximately 0.11 seconds (8259 lines/second)
Physical Source Lines of Code (SLOC) = 733
Hits@level = [0]   0 [1]   0 [2]   8 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   8 [1+]   8 [2+]   8 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 10.9141 [1+] 10.9141 [2+] 10.9141 [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.