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-chip-1.1/pscan_chip.cpp
Examining data/pscan-chip-1.1/fasta_to_raw.cpp

FINAL RESULTS:

data/pscan-chip-1.1/pscan_chip.cpp:209:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
				strcpy(add_argv[0], argv[0]);
data/pscan-chip-1.1/pscan_chip.cpp:211:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
				strcpy(add_argv[2], additional_matrix_backgroundfile.c_str());
data/pscan-chip-1.1/pscan_chip.cpp:213:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
				strcpy(add_argv[4], DEFAULT_BG_GENOME.c_str());
data/pscan-chip-1.1/pscan_chip.cpp:215:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
				strcpy(add_argv[6], additional_matrixfile.c_str());	
data/pscan-chip-1.1/fasta_to_raw.cpp:80:10:  [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).
				out2.open((fout.c_str()));
data/pscan-chip-1.1/pscan_chip.cpp:45:1:  [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];
data/pscan-chip-1.1/pscan_chip.cpp:189:13:  [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_out.open(outfile.c_str(), ios::out);
data/pscan-chip-1.1/pscan_chip.cpp:204:5:  [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 *add_argv[arg_num];
data/pscan-chip-1.1/pscan_chip.cpp:210:5:  [2] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant string.
				strcpy(add_argv[1], "-r");
data/pscan-chip-1.1/pscan_chip.cpp:212:5:  [2] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant string.
				strcpy(add_argv[3], "-g");
data/pscan-chip-1.1/pscan_chip.cpp:214:5:  [2] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant string.
				strcpy(add_argv[5], "-M");
data/pscan-chip-1.1/pscan_chip.cpp:457:2:  [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 Oligo[M->length() + 1];
data/pscan-chip-1.1/pscan_chip.cpp:741:8:  [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).
		out2.open(dist2_outfile.c_str());
data/pscan-chip-1.1/pscan_chip.cpp:742:8:  [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).
		out3.open(dist3_outfile.c_str());
data/pscan-chip-1.1/pscan_chip.cpp:1174:6:  [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(file.c_str());
data/pscan-chip-1.1/pscan_chip.cpp:1247:41:  [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).
                                RSIZE = atoi(argv[++i]);
data/pscan-chip-1.1/pscan_chip.cpp:474:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
		strncpy(Oligo, S->seq() + RSIZE/2 + (M->get_pos_at(i) - M->length()/2), M->length());
data/pscan-chip-1.1/pscan_chip.cpp:510:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
				strncpy(Oligo, S->seq() + RSIZE/2 + P, M->length());
data/pscan-chip-1.1/pscan_chip.cpp:522:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
				strncpy(Oligo, S->seq() + RSIZE/2 + P, M->length());

ANALYSIS SUMMARY:

Hits = 19
Lines analyzed = 2929 in approximately 0.08 seconds (38563 lines/second)
Physical Source Lines of Code (SLOC) = 1842
Hits@level = [0]   0 [1]   3 [2]  12 [3]   0 [4]   4 [5]   0
Hits@level+ = [0+]  19 [1+]  19 [2+]  16 [3+]   4 [4+]   4 [5+]   0
Hits/KSLOC@level+ = [0+] 10.3149 [1+] 10.3149 [2+] 8.68621 [3+] 2.17155 [4+] 2.17155 [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.