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/lambda-align2-2.0.0/src/lambda.cpp
Examining data/lambda-align2-2.0.0/src/mkindex.hpp
Examining data/lambda-align2-2.0.0/src/mkindex_algo.hpp
Examining data/lambda-align2-2.0.0/src/mkindex_misc.hpp
Examining data/lambda-align2-2.0.0/src/mkindex_options.hpp
Examining data/lambda-align2-2.0.0/src/mkindex_saca.hpp
Examining data/lambda-align2-2.0.0/src/search.hpp
Examining data/lambda-align2-2.0.0/src/search_datastructures.hpp
Examining data/lambda-align2-2.0.0/src/search_misc.hpp
Examining data/lambda-align2-2.0.0/src/search_options.hpp
Examining data/lambda-align2-2.0.0/src/search_output.hpp
Examining data/lambda-align2-2.0.0/src/shared_definitions.hpp
Examining data/lambda-align2-2.0.0/src/shared_misc.hpp
Examining data/lambda-align2-2.0.0/src/shared_options.hpp
Examining data/lambda-align2-2.0.0/src/search_algo.hpp

FINAL RESULTS:

data/lambda-align2-2.0.0/src/mkindex_misc.hpp:28:5:  [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 cwd[1000];
data/lambda-align2-2.0.0/src/search.hpp:249:14:  [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).
    int fd = open(toCString(options.output), O_WRONLY | O_CREAT | O_NOCTTY | O_NONBLOCK, 0600);
data/lambda-align2-2.0.0/src/search_algo.hpp:313:15:  [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).
        ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:335:11:  [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).
    ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:354:15:  [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).
        ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:379:15:  [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).
    int ret = open(globalHolder.dbIndex, path.c_str(), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:426:15:  [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).
    int ret = open(globalHolder.sTaxIds, path.c_str(), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:452:11:  [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).
    ret = open(globalHolder.taxParents, path.c_str(), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:458:11:  [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).
    ret = open(globalHolder.taxHeights, path.c_str(), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_algo.hpp:464:11:  [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).
    ret = open(globalHolder.taxNames, path.c_str(), OPEN_RDONLY);
data/lambda-align2-2.0.0/src/search_output.hpp:309:9:  [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).
        open(globalHolder.outfile, toCString(options.output));
data/lambda-align2-2.0.0/src/search_output.hpp:324:9:  [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).
        open(globalHolder.outfileBam, toCString(options.output));

ANALYSIS SUMMARY:

Hits = 12
Lines analyzed = 9595 in approximately 0.35 seconds (27289 lines/second)
Physical Source Lines of Code (SLOC) = 6944
Hits@level = [0]   0 [1]   0 [2]  12 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  12 [1+]  12 [2+]  12 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 1.72811 [1+] 1.72811 [2+] 1.72811 [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.