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/pscan-tfbs-1.2.2/pscan.cpp

FINAL RESULTS:

data/pscan-tfbs-1.2.2/pscan.cpp:1413:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system(d2u.str().c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:1423:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system(str1.str().c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:1442:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system(str2.str().c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:1443:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system("rm -f .tmp");
data/pscan-tfbs-1.2.2/pscan.cpp:52:7:  [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.
const char ALPHABET[4] = {'A','C','G','T'};
data/pscan-tfbs-1.2.2/pscan.cpp:53:7:  [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.
const char C_ALPHABET[4] = {'T','G','C','A'};
data/pscan-tfbs-1.2.2/pscan.cpp:57:1:  [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 VI['T' + 1], rc_VI['T' + 1];
data/pscan-tfbs-1.2.2/pscan.cpp:770:16:  [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).
				SPLIT[0] = atoi(argv[++i]);
data/pscan-tfbs-1.2.2/pscan.cpp:771:16:  [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).
				SPLIT[1] = atoi(argv[++i]);
data/pscan-tfbs-1.2.2/pscan.cpp:1426:5:  [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).
	in.open(tmpfile_1.c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:1621:8:  [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).
			out.open("pscan.complete_matrix");
data/pscan-tfbs-1.2.2/pscan.cpp:1627:8:  [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).
			out.open(buf.c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:1681:29:  [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).
                        out.open("pscan.short_matrix");
data/pscan-tfbs-1.2.2/pscan.cpp:1694:29:  [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).
                        out.open(buf.c_str());
data/pscan-tfbs-1.2.2/pscan.cpp:5727:7:  [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).
	fout.open("chip.fasta");
data/pscan-tfbs-1.2.2/pscan.cpp:5733:9:  [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).
		in[a].open(chip_files.at(a).c_str());

ANALYSIS SUMMARY:

Hits = 16
Lines analyzed = 6050 in approximately 0.13 seconds (45577 lines/second)
Physical Source Lines of Code (SLOC) = 3611
Hits@level = [0]   0 [1]   0 [2]  12 [3]   0 [4]   4 [5]   0
Hits@level+ = [0+]  16 [1+]  16 [2+]  16 [3+]   4 [4+]   4 [5+]   0
Hits/KSLOC@level+ = [0+] 4.43091 [1+] 4.43091 [2+] 4.43091 [3+] 1.10773 [4+] 1.10773 [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.