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/gffread-0.12.1/gff_utils.cpp
Examining data/gffread-0.12.1/gff_utils.h
Examining data/gffread-0.12.1/gffread.cpp

FINAL RESULTS:

data/gffread-0.12.1/gff_utils.cpp:223:3:  [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(charbuf, s.chars());
data/gffread-0.12.1/gff_utils.cpp:233:3:  [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(charbuf, seqid);
data/gffread-0.12.1/gff_utils.cpp:200:9:  [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.
 static char charbuf[128];
data/gffread-0.12.1/gff_utils.cpp:230:10:  [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.
  static char charbuf[128];
data/gffread-0.12.1/gff_utils.cpp:1286:10:  [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).
	FILE* f=fopen(flst.chars(), "r");
data/gffread-0.12.1/gff_utils.h:599:3:  [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 nt[3];
data/gffread-0.12.1/gff_utils.h:708:17:  [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 ((f=fopen(fname.chars(), "r"))==NULL) {
data/gffread-0.12.1/gffread.cpp:311:6:  [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).
			f=fopen(s,"w");
data/gffread-0.12.1/gffread.cpp:567:15:  [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).
       f_repl=fopen(s.chars(), "w");
data/gffread-0.12.1/gffread.cpp:613:13:  [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).
   FILE* ft=fopen(s,"r");
data/gffread-0.12.1/gffread.cpp:620:16:  [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).
   FILE* fsize=fopen(s,"r");
data/gffread-0.12.1/gffread.cpp:665:28:  [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).
           else  if ((f_in=fopen(infile, "r"))==NULL)
data/gffread-0.12.1/gff_utils.cpp:68:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
 int len=(seqlen>0)?seqlen:strlen(seq);
data/gffread-0.12.1/gff_utils.cpp:1289:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	slurp.read(f, NULL);

ANALYSIS SUMMARY:

Hits = 14
Lines analyzed = 3103 in approximately 0.12 seconds (25559 lines/second)
Physical Source Lines of Code (SLOC) = 2435
Hits@level = [0]  52 [1]   2 [2]  10 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+]  66 [1+]  14 [2+]  12 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 27.1047 [1+] 5.74949 [2+] 4.92813 [3+] 0.821355 [4+] 0.821355 [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.