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/spaced-1.2.0-201605+dfsg/src/variance.cpp
Examining data/spaced-1.2.0-201605+dfsg/src/variance.h
Examining data/spaced-1.2.0-201605+dfsg/src/patternset.h
Examining data/spaced-1.2.0-201605+dfsg/src/spaced.cc
Examining data/spaced-1.2.0-201605+dfsg/src/patternset.cpp
Examining data/spaced-1.2.0-201605+dfsg/src/sort.h

FINAL RESULTS:

data/spaced-1.2.0-201605+dfsg/src/patternset.cpp:355:2:  [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 tokens[6] = {'.', ' ', ',', ';', '\n', '\t'};
data/spaced-1.2.0-201605+dfsg/src/patternset.cpp:361:8:  [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).
	fasta.open(inFile);
data/spaced-1.2.0-201605+dfsg/src/sort.h:74:11:  [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.
	unsigned char alphabet[256]={};
data/spaced-1.2.0-201605+dfsg/src/sort.h:131:10:  [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).
	outfile.open(filename.c_str());
data/spaced-1.2.0-201605+dfsg/src/sort.h:161:11:  [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.
	unsigned char alphabet[256]={};
data/spaced-1.2.0-201605+dfsg/src/sort.h:512:11:  [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.
	unsigned char alphabet[256]={};
data/spaced-1.2.0-201605+dfsg/src/spaced.cc:78:22:  [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).
            weight = atoi(argv[++i]);
data/spaced-1.2.0-201605+dfsg/src/spaced.cc:86:24:  [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).
            dontcare = atoi(argv[++i]);
data/spaced-1.2.0-201605+dfsg/src/spaced.cc:94:22:  [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).
            number = atoi(argv[++i]);
data/spaced-1.2.0-201605+dfsg/src/spaced.cc:102:23:  [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).
            threads = atoi(argv[++i]);
data/spaced-1.2.0-201605+dfsg/src/spaced.cc:135:15:  [2] (misc) fopen:
  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).
	if (!(file = fopen(filename, "r"))) {
data/spaced-1.2.0-201605+dfsg/src/variance.cpp:621:16:  [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).
			pattern_out.open(outFile);

ANALYSIS SUMMARY:

Hits = 12
Lines analyzed = 3132 in approximately 0.09 seconds (33048 lines/second)
Physical Source Lines of Code (SLOC) = 2252
Hits@level = [0]  27 [1]   0 [2]  12 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  39 [1+]  12 [2+]  12 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 17.3179 [1+] 5.3286 [2+] 5.3286 [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.