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-align-1.0.3/src/holders.hpp
Examining data/lambda-align-1.0.3/src/lambda.cpp
Examining data/lambda-align-1.0.3/src/lambda.hpp
Examining data/lambda-align-1.0.3/src/lambda_indexer.cpp
Examining data/lambda-align-1.0.3/src/lambda_indexer.hpp
Examining data/lambda-align-1.0.3/src/lambda_indexer_misc.hpp
Examining data/lambda-align-1.0.3/src/match.hpp
Examining data/lambda-align-1.0.3/src/misc.hpp
Examining data/lambda-align-1.0.3/src/options.hpp
Examining data/lambda-align-1.0.3/src/output.hpp
Examining data/lambda-align-1.0.3/src/radix_inplace.h

FINAL RESULTS:

data/lambda-align-1.0.3/src/lambda.hpp:202:15:  [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-align-1.0.3/src/lambda.hpp:231:11:  [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-align-1.0.3/src/lambda.hpp:254:15:  [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-align-1.0.3/src/lambda.hpp:301:15:  [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-align-1.0.3/src/lambda.hpp:367:17:  [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).
        fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY);
data/lambda-align-1.0.3/src/lambda.hpp:369:21:  [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).
            fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY);
data/lambda-align-1.0.3/src/lambda_indexer.hpp:273:16:  [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).
        stream.open(toCString(options.segFile));
data/lambda-align-1.0.3/src/options.hpp:168:5:  [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-align-1.0.3/src/output.hpp:300:9:  [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-align-1.0.3/src/output.hpp:315:9:  [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 = 10
Lines analyzed = 6919 in approximately 0.20 seconds (34871 lines/second)
Physical Source Lines of Code (SLOC) = 4654
Hits@level = [0]   0 [1]   0 [2]  10 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  10 [1+]  10 [2+]  10 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 2.14869 [1+] 2.14869 [2+] 2.14869 [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.