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/caftools-2.0.3/src/caf2ace.c
Examining data/caftools-2.0.3/src/caf2fastq.c
Examining data/caftools-2.0.3/src/caf2gap.c
Examining data/caftools-2.0.3/src/caf2gap.h
Examining data/caftools-2.0.3/src/g-filedefs.h
Examining data/caftools-2.0.3/src/g-io.h
Examining data/caftools-2.0.3/src/g-os.h
Examining data/caftools-2.0.3/src/gap-dbstruct.h
Examining data/caftools-2.0.3/src/os.h
Examining data/caftools-2.0.3/src/caf2phrap.c
Examining data/caftools-2.0.3/src/caf_build_consensus.c
Examining data/caftools-2.0.3/src/caf_check_pads.c
Examining data/caftools-2.0.3/src/caf_check_pads.h
Examining data/caftools-2.0.3/src/caf_depad.c
Examining data/caftools-2.0.3/src/caf_pad.c
Examining data/caftools-2.0.3/src/cafcat.c
Examining data/caftools-2.0.3/src/cafmerge.c
Examining data/caftools-2.0.3/src/fix_quals.c
Examining data/caftools-2.0.3/src/nd_clip.c
Examining data/caftools-2.0.3/src/nd_edit.c
Examining data/caftools-2.0.3/src/ne_clip.c
Examining data/caftools-2.0.3/src/np_edit.c
Examining data/caftools-2.0.3/src/phd2scf.c
Examining data/caftools-2.0.3/src/phrapcons.c
Examining data/caftools-2.0.3/src/scf2phd.c
Examining data/caftools-2.0.3/src/sdict.c
Examining data/caftools-2.0.3/src/templates.c
Examining data/caftools-2.0.3/src/acedb/freesubs.c
Examining data/caftools-2.0.3/src/acedb/freeout.c
Examining data/caftools-2.0.3/src/acedb/messclean.c
Examining data/caftools-2.0.3/src/acedb/arraysub.c
Examining data/caftools-2.0.3/src/acedb/filsubs.c
Examining data/caftools-2.0.3/src/acedb/timesubs.c
Examining data/caftools-2.0.3/src/acedb/randsubs.c
Examining data/caftools-2.0.3/src/acedb/call.c
Examining data/caftools-2.0.3/src/acedb/filqng.c
Examining data/caftools-2.0.3/src/acedb/dict.c
Examining data/caftools-2.0.3/src/acedb/acedb.h
Examining data/caftools-2.0.3/src/acedb/call.h
Examining data/caftools-2.0.3/src/acedb/freeout.h
Examining data/caftools-2.0.3/src/acedb/mydirent.h
Examining data/caftools-2.0.3/src/acedb/mytime.h
Examining data/caftools-2.0.3/src/acedb/array.h
Examining data/caftools-2.0.3/src/acedb/dict.h
Examining data/caftools-2.0.3/src/acedb/keyset.h
Examining data/caftools-2.0.3/src/acedb/mystdlib.h
Examining data/caftools-2.0.3/src/acedb/regular.h
Examining data/caftools-2.0.3/src/acedb/messubs.c
Examining data/caftools-2.0.3/src/libsrc/cafseq.c
Examining data/caftools-2.0.3/src/libsrc/cafstrings.c
Examining data/caftools-2.0.3/src/libsrc/assembly.c
Examining data/caftools-2.0.3/src/libsrc/base_edit.c
Examining data/caftools-2.0.3/src/libsrc/seq_util.c
Examining data/caftools-2.0.3/src/libsrc/clipping.c
Examining data/caftools-2.0.3/src/libsrc/consensus.c
Examining data/caftools-2.0.3/src/libsrc/fix_tags.c
Examining data/caftools-2.0.3/src/libsrc/cafbin.c
Examining data/caftools-2.0.3/src/libsrc/padding.c
Examining data/caftools-2.0.3/src/libsrc/caf_check.c
Examining data/caftools-2.0.3/src/libsrc/pair_memory.c
Examining data/caftools-2.0.3/src/libsrc/assinf.c
Examining data/caftools-2.0.3/src/libsrc/auto_edit.h
Examining data/caftools-2.0.3/src/libsrc/bases.h
Examining data/caftools-2.0.3/src/libsrc/caf.h
Examining data/caftools-2.0.3/src/libsrc/caf_types.h
Examining data/caftools-2.0.3/src/libsrc/cafseq.h
Examining data/caftools-2.0.3/src/libsrc/cl.h
Examining data/caftools-2.0.3/src/libsrc/myscf.h
Examining data/caftools-2.0.3/src/libsrc/padding.h
Examining data/caftools-2.0.3/src/libsrc/pair_memory.h
Examining data/caftools-2.0.3/src/libsrc/seq_util.h
Examining data/caftools-2.0.3/src/libsrc/sw.h
Examining data/caftools-2.0.3/src/libsrc/trace_edit.h
Examining data/caftools-2.0.3/src/libsrc/tree.h
Examining data/caftools-2.0.3/src/libsrc/caf_check.h
Examining data/caftools-2.0.3/src/libsrc/consensus.h
Examining data/caftools-2.0.3/src/libsrc/assinf.h
Examining data/caftools-2.0.3/src/libsrc/readline.c
Examining data/caftools-2.0.3/src/libsrc/cl.c
Examining data/caftools-2.0.3/src/libsrc/readline.h
Examining data/caftools-2.0.3/src/libsrc/complement_scf.c
Examining data/caftools-2.0.3/src/libsrc/trace_align.c
Examining data/caftools-2.0.3/src/libsrc/trace_quality.c
Examining data/caftools-2.0.3/src/libsrc/caf_read_scf.c
Examining data/caftools-2.0.3/src/libsrc/scf_cache.c
Examining data/caftools-2.0.3/src/libsrc/classify.c
Examining data/caftools-2.0.3/src/libsrc/trace_align.h
Examining data/caftools-2.0.3/src/libsrc/trace_quality.h
Examining data/caftools-2.0.3/src/libsrc/tree_util.c
Examining data/caftools-2.0.3/src/libsrc/sgrep.c
Examining data/caftools-2.0.3/src/libsrc/sw.c
Examining data/caftools-2.0.3/src/libsrc/seq_dict.c
Examining data/caftools-2.0.3/src/libsrc/lin_align.c
Examining data/caftools-2.0.3/src/libsrc/banded.c
Examining data/caftools-2.0.3/src/libsrc/wordhash.c
Examining data/caftools-2.0.3/src/libsrc/bases.c
Examining data/caftools-2.0.3/src/libsrc/cmp.h
Examining data/caftools-2.0.3/src/libsrc/lin_align.h
Examining data/caftools-2.0.3/src/libsrc/seq_dict.h
Examining data/caftools-2.0.3/src/libsrc/wordhash.h
Examining data/caftools-2.0.3/src/libsrc/searchpath.c
Examining data/caftools-2.0.3/src/libsrc/seed.c
Examining data/caftools-2.0.3/src/libsrc/cmp.c
Examining data/caftools-2.0.3/src/libsrc/dir.c
Examining data/caftools-2.0.3/src/libsrc/priority_queue.c
Examining data/caftools-2.0.3/src/libsrc/ncr.c
Examining data/caftools-2.0.3/src/libsrc/ncr.h
Examining data/caftools-2.0.3/src/libsrc/priority_queue.h

FINAL RESULTS:

data/caftools-2.0.3/src/acedb/call.c:119:10:  [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.
  return system (buildCommand (dir, script, args)) ;
data/caftools-2.0.3/src/acedb/call.c:133:10:  [4] (shell) popen:
  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.
  return popen (buildCommand (dir, script, args), "r" ) ;
data/caftools-2.0.3/src/acedb/call.c:234:4:  [4] (shell) execlp:
  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.
	  execlp (buildCommand (0, "Mosaic", 0),
data/caftools-2.0.3/src/acedb/filsubs.c:131:7:  [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 (fullpath, dir) ;
data/caftools-2.0.3/src/acedb/filsubs.c:140:7:  [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 (fullpath, drive) ;
data/caftools-2.0.3/src/acedb/filsubs.c:141:7:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
      strcat (fullpath, dir) ;
data/caftools-2.0.3/src/acedb/filsubs.c:149:7:  [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 (fullpath, pwd) ;
data/caftools-2.0.3/src/acedb/filsubs.c:150:7:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
      strcat (fullpath, SUBDIR_DELIMITER_STR) ;
data/caftools-2.0.3/src/acedb/filsubs.c:151:7:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
      strcat (fullpath, dir) ;
data/caftools-2.0.3/src/acedb/filsubs.c:177:16:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      return !(access (name, R_OK)) ;
data/caftools-2.0.3/src/acedb/filsubs.c:180:12:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      if (!access (name, W_OK))	/* requires file exists */
data/caftools-2.0.3/src/acedb/filsubs.c:187:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
	return !(access (".", W_OK)) ;
data/caftools-2.0.3/src/acedb/filsubs.c:190:15:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
	  result = !(access (name, W_OK)) ;
data/caftools-2.0.3/src/acedb/filsubs.c:195:16:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      return !(access (name, X_OK)) ;
data/caftools-2.0.3/src/acedb/filsubs.c:427:3:  [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 (entryPathName, dirName) ;
data/caftools-2.0.3/src/acedb/filsubs.c:440:7:  [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 (leaf, dName) ;
data/caftools-2.0.3/src/acedb/filsubs.c:502:3:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
		strcat(cwd, SUBDIR_DELIMITER_STR) ; /* then tack on a SUBDIR_DELIMITER*/
data/caftools-2.0.3/src/acedb/filsubs.c:503:8:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	      strcat(cwd, path) ;
data/caftools-2.0.3/src/acedb/filsubs.c:521:6:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	    strcat(cwd, SUBDIR_DELIMITER_STR) ; /* then tack on a SUBDIR_DELIMITER */
data/caftools-2.0.3/src/acedb/filsubs.c:522:4:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	  strcat(cwd, path) ;
data/caftools-2.0.3/src/acedb/freeout.c:220:19:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  DLL_LINKAGE int vfprintf (FILE *stream, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:221:19:  [4] (buffer) vfscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vfscanf  (FILE *stream, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:222:19:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  DLL_LINKAGE int vprintf  (const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:223:19:  [4] (buffer) vscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vscanf   (const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:224:19:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
  DLL_LINKAGE int vsprintf (char *buffer, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:225:19:  [4] (buffer) vsscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vsscanf  (const char *buffer, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/freeout.c:235:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf (outBuf,format,args) ;
data/caftools-2.0.3/src/acedb/freesubs.c:100:5:  [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 (stream[streamlevel].special, text) ;
data/caftools-2.0.3/src/acedb/freesubs.c:130:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf (!currfil ? "From text >" : "From file >") ;
data/caftools-2.0.3/src/acedb/freesubs.c:229:7:  [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 ((char*)pos) ;
data/caftools-2.0.3/src/acedb/freesubs.c:338:3:  [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 (stream[streamlevel].special, stream[streamlevel-1].special) ;
data/caftools-2.0.3/src/acedb/messubs.c:74:19:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  DLL_LINKAGE int vfprintf (FILE *stream, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:75:19:  [4] (buffer) vfscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vfscanf  (FILE *stream, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:76:19:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  DLL_LINKAGE int vprintf  (const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:77:19:  [4] (buffer) vscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vscanf   (const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:78:19:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
  DLL_LINKAGE int vsprintf (char *buffer, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:79:19:  [4] (buffer) vsscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  DLL_LINKAGE int vsscanf  (const char *buffer, const char *format, va_list arglist);
data/caftools-2.0.3/src/acedb/messubs.c:120:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf (messbuf,format,args) ;
data/caftools-2.0.3/src/acedb/messubs.c:238:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vfprintf (dumpfil, format, args) ;
data/caftools-2.0.3/src/acedb/messubs.c:279:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf (messbuf2,format,args) ;
data/caftools-2.0.3/src/acedb/messubs.c:326:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf (crashText, format, args) ;
data/caftools-2.0.3/src/acedb/messubs.c:367:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf (messbuf,format,args) ;
data/caftools-2.0.3/src/acedb/messubs.c:506:7:  [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(result, old);
data/caftools-2.0.3/src/acedb/timesubs.c:431:2:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	strcat (buf, messprintf ("%d", ddiff)) ;
data/caftools-2.0.3/src/acedb/timesubs.c:434:6:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	    strcat (buf, messprintf ("%d_", ddiff)) ;
data/caftools-2.0.3/src/acedb/timesubs.c:435:4:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	  strcat (buf, messprintf ("%02d:%02d", hdiff, mindiff)) ;
data/caftools-2.0.3/src/acedb/timesubs.c:437:6:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	    strcat (buf, messprintf (":%02d", sdiff)) ;
data/caftools-2.0.3/src/acedb/timesubs.c:444:2:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	strcat (buf, messprintf ("%d-%02d-0", ydiff, mdiff)) ;
data/caftools-2.0.3/src/acedb/timesubs.c:446:2:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	strcat (buf, messprintf ("%d-0", mdiff)) ;
data/caftools-2.0.3/src/caf2gap.c:1483:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(arrp(new_comment, 0, char),
data/caftools-2.0.3/src/caf2phrap.c:213:4:  [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(qualfile,outfile);
data/caftools-2.0.3/src/caf2phrap.c:242:8:  [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(cafout, outfile);
data/caftools-2.0.3/src/caf2phrap.c:252:5:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
		  sscanf(line, "%s", read );
data/caftools-2.0.3/src/caf2phrap.c:563:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(description, "DIRECTION: %s CHEM: %s DYE: %s TEMPLATE: %s",
data/caftools-2.0.3/src/cafcat.c:149:5:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
				sscanf(line, "%s", read);
data/caftools-2.0.3/src/libsrc/assembly.c:990:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(buf,"%s~", name);
data/caftools-2.0.3/src/libsrc/base_edit.c:229:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf( text, " masked badly aligned read %s  similarity with consensus = %.2f",   
data/caftools-2.0.3/src/libsrc/base_edit.c:235:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf( text, 	" badly aligned read %s  similarity with consensus = %.2f",  
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:555:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(fext, "%s%s", fn, magics[i].extension);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:588:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(buf, "%s %s 2>/dev/null",
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:592:15:  [4] (shell) popen:
  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.
      	return popen(buf, "r");
data/caftools-2.0.3/src/libsrc/cafbin.c:261:7:  [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(s,buffer);
data/caftools-2.0.3/src/libsrc/cafbin.c:425:8:  [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(tag->text,buffer);
data/caftools-2.0.3/src/libsrc/cafseq.c:188:4:  [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 (class, word) ;
data/caftools-2.0.3/src/libsrc/cafseq.c:193:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf(msg,"No object name after class name: %s :", class) ;
data/caftools-2.0.3/src/libsrc/cl.c:80:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s", format);
data/caftools-2.0.3/src/libsrc/cl.c:82:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s%s", format, "=%f");
data/caftools-2.0.3/src/libsrc/cl.c:86:12:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
      if ( sscanf( argv[argc], Format, &t ) == 1 ) 
data/caftools-2.0.3/src/libsrc/cl.c:151:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s", format);
data/caftools-2.0.3/src/libsrc/cl.c:153:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s%s", format, "=%d");
data/caftools-2.0.3/src/libsrc/cl.c:157:12:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
      if ( sscanf( argv[argc], Format, &t ) == 1 ) 
data/caftools-2.0.3/src/libsrc/cl.c:259:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(noformat,"-no%s", &format[1] );
data/caftools-2.0.3/src/libsrc/cl.c:261:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(noformat,"-no%s", format );
data/caftools-2.0.3/src/libsrc/cl.c:305:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s", format);
data/caftools-2.0.3/src/libsrc/cl.c:307:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(Format,"%s%s", format, "=%s");
data/caftools-2.0.3/src/libsrc/cl.c:311:7:  [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(arg, s);
data/caftools-2.0.3/src/libsrc/cl.c:316:12:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
      if ( sscanf( argv[argc], Format, arg ) > 0 ) return 1;
data/caftools-2.0.3/src/libsrc/cl.c:341:8:  [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( filename, argv[argc] );
data/caftools-2.0.3/src/libsrc/cl.c:398:3:  [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( &filename[n], ext );
data/caftools-2.0.3/src/libsrc/cl.c:484:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf( name, "%s/%s", dir, filename );
data/caftools-2.0.3/src/libsrc/cl.c:486:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf( name, "%s%s", dir, filename );
data/caftools-2.0.3/src/libsrc/cl.c:488:7:  [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( filename, name );
data/caftools-2.0.3/src/libsrc/cl.c:652:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	  sprintf( date, "%s", ctime(&buf.st_mtime) );
data/caftools-2.0.3/src/libsrc/dir.c:57:4:  [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(name,fil->d_name);
data/caftools-2.0.3/src/libsrc/dir.c:106:4:  [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(name,fil->d_name);
data/caftools-2.0.3/src/libsrc/lin_align.c:1071:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	  fprintf(fp, format, genome->name, gcoord[i]+1 );
data/caftools-2.0.3/src/libsrc/lin_align.c:1082:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	  fprintf(fp, format, est->name, ecoord[i]+1 );
data/caftools-2.0.3/src/libsrc/searchpath.c:43:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	  sprintf(fullname,"%s/%s", p, basename );
data/caftools-2.0.3/src/libsrc/searchpath.c:53:7:  [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( fullname, basename );
data/caftools-2.0.3/src/libsrc/seq_dict.c:197:3:  [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(buf,db);
data/caftools-2.0.3/src/libsrc/seq_dict.c:204:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      if (  fscanf(fp, "%d\n%d\n%s\n%d\n", &seqdict->wordsize, &seqdict->prime, db, &seqdict->sequences ) != 4 )
data/caftools-2.0.3/src/libsrc/seq_dict.c:223:4:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	  fscanf(fp, "%d %s\n", &i, name );
data/caftools-2.0.3/src/libsrc/seq_util.c:54:3:  [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(buf,basename);
data/caftools-2.0.3/src/libsrc/seq_util.c:164:6:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	    strcat( buf, clean_line(line)+strlen(key) );
data/caftools-2.0.3/src/libsrc/seq_util.c:199:3:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
		strcat( buf, clean_line(line)+strlen(key) );
data/caftools-2.0.3/src/libsrc/seq_util.c:294:10:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  while( fscanf( db->indexfile, "%s %lu\n", name, &offset ) == 2 )
data/caftools-2.0.3/src/libsrc/seq_util.c:326:10:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  while( fscanf( db->indexfile, "%s %lu\n", name, &offset ) == 2 )
data/caftools-2.0.3/src/libsrc/seq_util.c:357:10:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  while( fscanf( db->indexfile, "%s %lu %lu\n", name, &offset1, &offset2 ) == 3 )
data/caftools-2.0.3/src/libsrc/seq_util.c:444:3:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  sscanf( line, "ID  %s", sname );
data/caftools-2.0.3/src/libsrc/seq_util.c:558:3:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  sscanf( line, ">%s", sname );
data/caftools-2.0.3/src/libsrc/seq_util.c:603:3:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  sscanf( line, ">>>>%s", sname );
data/caftools-2.0.3/src/libsrc/seq_util.c:699:4:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	  fscanf( datafile, "%s", sname ); 
data/caftools-2.0.3/src/libsrc/seq_util.c:749:4:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
	  fscanf( datafile, "%s", sname ); 
data/caftools-2.0.3/src/libsrc/seq_util.c:786:7:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      fscanf( datafile, ">>>>%s", name1 );
data/caftools-2.0.3/src/libsrc/seq_util.c:787:7:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      fscanf( textfile, ">>>>%s", name2 );
data/caftools-2.0.3/src/libsrc/seq_util.c:897:7:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      sscanf( line, "%s", seq );
data/caftools-2.0.3/src/libsrc/seq_util.c:913:7:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      sscanf( line, "%s", name );
data/caftools-2.0.3/src/libsrc/seq_util.c:931:7:  [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(buf,spec);
data/caftools-2.0.3/src/libsrc/seq_util.c:950:3:  [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(wild,old_wild);
data/caftools-2.0.3/src/libsrc/seq_util.c:1185:4:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	  strcat( regexp, s );
data/caftools-2.0.3/src/libsrc/seq_util.c:1248:7:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      sscanf( desc, "%s", name );
data/caftools-2.0.3/src/libsrc/trace_quality.c:1758:8:  [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(seq->SCF_File,dictName(Ass->seqDict,seq->id) );
data/caftools-2.0.3/src/libsrc/tree_util.c:255:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf( buf, "%s_%d", name, id );
data/caftools-2.0.3/src/libsrc/wordhash.c:46:12:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
      if ( sscanf( line, "%s", word ) == 1 )
data/caftools-2.0.3/src/nd_edit.c:507:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(text, "AUTO-EDIT: replaced %c by %c at %d (%s, %s, %s)", 
data/caftools-2.0.3/src/nd_edit.c:511:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(text, "AUTO-EDIT: deleted %c at %d  (%s, %s, %s)",
data/caftools-2.0.3/src/nd_edit.c:515:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf( text, "AUTO-EDIT: inserted %c at %d  (%s, %s, %s)",
data/caftools-2.0.3/src/nd_edit.c:522:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
		      sprintf( text, "AUTO-EDIT: unclear edit at %d (%s, %s %s)", edit->pos,  strand_text[edit->stranded], compound_text[edit->compound], Consensus_text[edit->consensus]);
data/caftools-2.0.3/src/nd_edit.c:528:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf( text, "AUTO-EDIT: Propose replace %c by %c at %d (%s, %s, %s)", 
data/caftools-2.0.3/src/nd_edit.c:532:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(text, "AUTO-EDIT: Propose delete %c at %d on (%s, %s, %s)",
data/caftools-2.0.3/src/nd_edit.c:536:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(text, "AUTO-EDIT: Propose insert %c at %d (%s, %s, %s)",
data/caftools-2.0.3/src/phd2scf.c:12:46:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
static void file_open_barf(char *name, char *access);
data/caftools-2.0.3/src/phd2scf.c:152:46:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
static void file_open_barf(char *name, char *access)
data/caftools-2.0.3/src/phd2scf.c:158:16:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
	  prog, name, access, errmsg);
data/caftools-2.0.3/src/scf2phd.c:35:46:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
static void file_open_barf(char *name, char *access);
data/caftools-2.0.3/src/scf2phd.c:127:46:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
static void file_open_barf(char *name, char *access)
data/caftools-2.0.3/src/scf2phd.c:133:16:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
	  prog, name, access, errmsg);
data/caftools-2.0.3/src/scf2phd.c:170:5:  [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(phd, line);
data/caftools-2.0.3/src/sdict.c:132:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(bufferfile, "%s/buffer.temp", tmpdir );
data/caftools-2.0.3/src/sdict.c:316:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf(bufferfile2,"%s/%s.%d",tmpdir, bufferfile,n);
data/caftools-2.0.3/src/sdict.c:334:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf(bufferfile2,"%s/%s.%d",tmpdir,bufferfile,i);
data/caftools-2.0.3/src/sdict.c:338:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf(bufferfile3,"%s/%s.%d",tmpdir,bufferfile,j);
data/caftools-2.0.3/src/sdict.c:343:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	      sprintf(mergefile,"%s/merged", tmpdir );
data/caftools-2.0.3/src/sdict.c:384:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(bufferfile2,"%s.%d",bufferfile,0);
data/caftools-2.0.3/src/sdict.c:387:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(triple_file,"%s/merged.tmp",tmpdir);
data/caftools-2.0.3/src/sdict.c:632:3:  [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(tmpfile,tempnam(tmpdir,"sdict")); /* temp filename */
data/caftools-2.0.3/src/acedb/filsubs.c:79:11:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
		(home = getenv (HOME_DIR_ENVP))) /* substitute */
data/caftools-2.0.3/src/acedb/filsubs.c:83:15:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      drive = getenv ("HOMEDRIVE") ;
data/caftools-2.0.3/src/acedb/filsubs.c:321:20:  [3] (tmpfile) tempnam:
  Temporary file race condition (CWE-377).
  if (!(*nameptr = tempnam ("/var/tmp", "ACEDB")))
data/caftools-2.0.3/src/acedb/filsubs.c:515:18:  [3] (buffer) getwd:
  This does not protect against buffer overflows by itself, so use with
  caution (CWE-120, CWE-20). Use getcwd instead.
      if( (cwd = getwd(cwdpath)) != NULL )	/* If a non-NULL current working */
data/caftools-2.0.3/src/acedb/mydirent.h:58:9:  [3] (buffer) getwd:
  This does not protect against buffer overflows by itself, so use with
  caution (CWE-120, CWE-20). Use getcwd instead.
#define getwd(buf) getcwd(buf,MAXPATHLEN - 2) 
data/caftools-2.0.3/src/acedb/mydirent.h:60:14:  [3] (buffer) getwd:
  This does not protect against buffer overflows by itself, so use with
  caution (CWE-120, CWE-20). Use getcwd instead.
extern char *getwd(char *pathname) ;
data/caftools-2.0.3/src/acedb/randsubs.c:40:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
{ extern int random (void) ;
data/caftools-2.0.3/src/acedb/randsubs.c:42:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   return random() ;
data/caftools-2.0.3/src/libsrc/searchpath.c:67:50:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return openfile_in_searchpath( basename, mode, getenv(env), fullname );
data/caftools-2.0.3/src/libsrc/seq_util.c:1336:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      m = random() % len;
data/caftools-2.0.3/src/scf2phd.c:98:29:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  if (NULL != (param_file = getenv("PHRED_PARAMETER_FILE"))) {
data/caftools-2.0.3/src/sdict.c:632:18:  [3] (tmpfile) tempnam:
  Temporary file race condition (CWE-377).
  strcpy(tmpfile,tempnam(tmpdir,"sdict")); /* temp filename */
data/caftools-2.0.3/src/acedb/arraysub.c:239:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy (new,a->base,a->size*a->max) ;
data/caftools-2.0.3/src/acedb/arraysub.c:295:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(b->base, a->base, a->max * a->size);
data/caftools-2.0.3/src/acedb/arraysub.c:316:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	  memcpy(b->base, a->base + x1, b->max * b->size);
data/caftools-2.0.3/src/acedb/arraysub.c:558:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(s->a->base, a->base, n) ;
data/caftools-2.0.3/src/acedb/call.c:211:10:  [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 MosaicPID[32] = {0}; /* string form of M_pid */
data/caftools-2.0.3/src/acedb/call.c:245:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	  sprintf (MosaicPID, "%d", M_pid) ;
data/caftools-2.0.3/src/acedb/filqng.c:42:14:  [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).
      (fil = fopen (stackText(s,i), "r")))
data/caftools-2.0.3/src/acedb/filqng.c:49:15:  [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 ((fil = fopen (stackText(s,i), spec)) != 0)
data/caftools-2.0.3/src/acedb/filqng.c:57:20:  [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 (!(fil = fopen (stackText(s,i), spec))) 
data/caftools-2.0.3/src/acedb/filsubs.c:126:3:  [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 dirbuf[DIR_BUFFER_SIZE] ;
data/caftools-2.0.3/src/acedb/filsubs.c:138:7:  [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.
    { char drive[3] = { GET_CURRENT_DRIVE, DRIVE_DELIMITER, '\0' } ;
data/caftools-2.0.3/src/acedb/filsubs.c:215:9:  [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 buf[DIR_BUFFER_SIZE] ;
data/caftools-2.0.3/src/acedb/filsubs.c:304:23:  [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 (!(result = fopen (s, spec)))
data/caftools-2.0.3/src/acedb/filsubs.c:415:3:  [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	*dName, entryPathName[MAXPATHLEN], *leaf ;
data/caftools-2.0.3/src/acedb/filsubs.c:472:10:  [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 newFilName[MAXPATHLEN] ;
data/caftools-2.0.3/src/acedb/filsubs.c:473:3:  [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 cwdpath[MAXPATHLEN], *cwd ;
data/caftools-2.0.3/src/acedb/freeout.c:209:8:  [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 outBuf [BUFSIZE] ;  /* buffer for messages */
data/caftools-2.0.3/src/acedb/freesubs.c:33:5:  [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 special[24] ;
data/caftools-2.0.3/src/acedb/freesubs.c:81:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy (card, oldCard, maxcard/2) ;
data/caftools-2.0.3/src/acedb/freesubs.c:91:8:  [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 special[256] ;
data/caftools-2.0.3/src/acedb/messubs.c:93:8:  [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 messbuf[BUFSIZE] ;	/* buffer for messages */
data/caftools-2.0.3/src/acedb/messubs.c:205:3:  [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 buf[100];
data/caftools-2.0.3/src/acedb/messubs.c:220:12:  [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).
	dumpfil = fopen(messdumpfilename, "a");
data/caftools-2.0.3/src/acedb/messubs.c:324:3:  [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 (messbuf, "FATAL ERROR: ") ;
data/caftools-2.0.3/src/acedb/timesubs.c:295:10:  [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 ace_time[25] ;
data/caftools-2.0.3/src/acedb/timesubs.c:320:10:  [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 ace_time[25] ;
data/caftools-2.0.3/src/acedb/timesubs.c:389:10:  [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 buf[25] ;
data/caftools-2.0.3/src/caf2ace.c:28:3:  [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 comp[5];
data/caftools-2.0.3/src/caf2ace.c:84:3:  [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 CAFfile[256] = {0};
data/caftools-2.0.3/src/caf2ace.c:240:3:  [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 b[51];
data/caftools-2.0.3/src/caf2ace.c:267:3:  [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 buffer[1056], *s, *t, *dna;
data/caftools-2.0.3/src/caf2ace.c:364:3:  [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 readname[100] = {0};
data/caftools-2.0.3/src/caf2ace.c:544:10:  [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 tab[256] = {0};
data/caftools-2.0.3/src/caf2ace.c:579:10:  [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 mx[256];
data/caftools-2.0.3/src/caf2fastq.c:26:3:  [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 caffile[256];
data/caftools-2.0.3/src/caf2fastq.c:27:3:  [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 mates_file[256]     = {0};
data/caftools-2.0.3/src/caf2fastq.c:28:3:  [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 templates_file[256] = {0};
data/caftools-2.0.3/src/caf2fastq.c:29:3:  [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 direction_file[256] = {0};
data/caftools-2.0.3/src/caf2fastq.c:30:3:  [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 out_file[256]       = {0};
data/caftools-2.0.3/src/caf2fastq.c:199:11:  [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).
  mates = fopen(mates_file, "w");
data/caftools-2.0.3/src/caf2fastq.c:261:15:  [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).
  templates = fopen(templates_file, "w");
data/caftools-2.0.3/src/caf2fastq.c:301:15:  [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).
  direction = fopen(direction_file, "w");
data/caftools-2.0.3/src/caf2gap.c:86:31:  [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.
      arr(buf,i*N+j,char) = ((char *)a)[i*N+(N-j-1)];
data/caftools-2.0.3/src/caf2gap.c:181:3:  [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 image[MAX_FILENAME_LEN * 2 + 2];    /* Name of image file */
data/caftools-2.0.3/src/caf2gap.c:182:3:  [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 aux[MAX_FILENAME_LEN * 2 + 6];      /* Name of aux file   */
data/caftools-2.0.3/src/caf2gap.c:227:24:  [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).
  if (-1 == (fdimage = open(image, oflag, S_DEFFILEMODE)))
data/caftools-2.0.3/src/caf2gap.c:233:24:  [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).
  if (-1 == (fdaux   = open(aux,   oflag, S_DEFFILEMODE)))
data/caftools-2.0.3/src/caf2gap.c:1131:12:  [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 mx[256];
data/caftools-2.0.3/src/caf2gap.c:1166:10:  [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 mx[256];
data/caftools-2.0.3/src/caf2gap.c:1413:12:  [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 t[sizeof(GCardinal)];
data/caftools-2.0.3/src/caf2gap.c:1416:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&t[0],s,len);
data/caftools-2.0.3/src/caf2gap.c:2240:3:  [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 project[MAX_FILENAME_LEN] = {0};/* project to create                  */
data/caftools-2.0.3/src/caf2gap.c:2241:3:  [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 version[MAX_FILENAME_LEN] = {0};/* version to create                  */
data/caftools-2.0.3/src/caf2gap.c:2242:3:  [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 acefile[MAX_FILENAME_LEN] = {0};/* caf file to read                   */
data/caftools-2.0.3/src/caf2gap.c:2250:3:  [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(acefile,"stdin");
data/caftools-2.0.3/src/caf2phrap.c:79:3:  [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 caffile[256];
data/caftools-2.0.3/src/caf2phrap.c:80:3:  [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 outfile[256];
data/caftools-2.0.3/src/caf2phrap.c:81:3:  [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 fofnfile[256];
data/caftools-2.0.3/src/caf2phrap.c:82:3:  [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 qualfile[256];
data/caftools-2.0.3/src/caf2phrap.c:83:3:  [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 cafout[256];
data/caftools-2.0.3/src/caf2phrap.c:84:3:  [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 read[256];
data/caftools-2.0.3/src/caf2phrap.c:85:3:  [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 line[256];
data/caftools-2.0.3/src/caf2phrap.c:100:3:  [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 clip[256], tag_mask[256];
data/caftools-2.0.3/src/caf2phrap.c:146:3:  [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(clip, "QUAL"); /* default quality clipping */
data/caftools-2.0.3/src/caf2phrap.c:214:4:  [2] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused). Risk is low because the
  source is a constant string.
	  strcat(qualfile,".qual");
data/caftools-2.0.3/src/caf2phrap.c:243:8:  [2] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused). Risk is low because the
  source is a constant string.
	      strcat(cafout, ".caf");
data/caftools-2.0.3/src/caf2phrap.c:513:4:  [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 description[1024];
data/caftools-2.0.3/src/caf2phrap.c:548:3:  [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 name_copy[256];
data/caftools-2.0.3/src/caf_build_consensus.c:11:3:  [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 input_file[256]  = {0};
data/caftools-2.0.3/src/caf_build_consensus.c:12:3:  [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 output_file[256] = {0};
data/caftools-2.0.3/src/caf_build_consensus.c:23:5:  [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(input_file, "stdin");
data/caftools-2.0.3/src/caf_build_consensus.c:27:5:  [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(output_file, "stdout");
data/caftools-2.0.3/src/caf_check_pads.c:14:3:  [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 CAFfile[256] = {0};
data/caftools-2.0.3/src/caf_check_pads.c:85:3:  [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 string[256];
data/caftools-2.0.3/src/caf_check_pads.c:240:11:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
          sprintf(string,"Consensus suggests %d %c's, Reads suggest %d",match_j-dash,base[y],maxMatch);
data/caftools-2.0.3/src/caf_check_pads.c:388:10:  [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 tab[256] = {0};
data/caftools-2.0.3/src/caf_depad.c:35:3:  [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 CAFfile[256];
data/caftools-2.0.3/src/caf_pad.c:41:3:  [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 filename[256];
data/caftools-2.0.3/src/cafcat.c:71:2:  [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 CAFfile[256];
data/caftools-2.0.3/src/cafcat.c:72:2:  [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 outfile[256];
data/caftools-2.0.3/src/cafcat.c:73:2:  [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 fofnfile[256];
data/caftools-2.0.3/src/cafcat.c:81:2:  [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(CAFfile, "stdin");
data/caftools-2.0.3/src/cafcat.c:82:2:  [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(outfile, "stdout");
data/caftools-2.0.3/src/cafcat.c:132:4:  [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 read[256];
data/caftools-2.0.3/src/cafcat.c:133:4:  [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 line[256];
data/caftools-2.0.3/src/cafmerge.c:83:3:  [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 caffile1[256], caffile2[256];
data/caftools-2.0.3/src/cafmerge.c:92:3:  [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 outfile[256];
data/caftools-2.0.3/src/fix_quals.c:12:3:  [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 assembly_file[256] = { 0 };
data/caftools-2.0.3/src/fix_quals.c:13:3:  [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 raw_file[256] = { 0 };
data/caftools-2.0.3/src/libsrc/assembly.c:982:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/auto_edit.h:130:8:  [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.
extern char *status_text[status_count]; 
data/caftools-2.0.3/src/libsrc/auto_edit.h:131:8:  [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.
extern char *compound_text[compound_count];
data/caftools-2.0.3/src/libsrc/auto_edit.h:132:8:  [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.
extern char *strand_text[strand_count];
data/caftools-2.0.3/src/libsrc/auto_edit.h:133:8:  [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.
extern char *TAG_text[status_count];
data/caftools-2.0.3/src/libsrc/auto_edit.h:134:8:  [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.
extern char *Consensus_text[Consensus_count];
data/caftools-2.0.3/src/libsrc/base_edit.c:212:3:  [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 text[256];
data/caftools-2.0.3/src/libsrc/base_edit.c:311:3:  [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 stolen[nucleotides];
data/caftools-2.0.3/src/libsrc/base_edit.c:312:3:  [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 native[nucleotides];
data/caftools-2.0.3/src/libsrc/bases.c:61:10:  [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 cbase[256];
data/caftools-2.0.3/src/libsrc/caf.h:90:8:  [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.
extern char *sequence_text[sequence_types];
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:232:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(samples_out, curr_sample, num_samples);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:240:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(samples_out, curr_sample, num_samples);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:248:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(samples_out, curr_sample, num_samples);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:256:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(samples_out, curr_sample, num_samples);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:326:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(c, comments_data, s);
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:448:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&scf->header, &h, sizeof(Header));
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:508:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(scf->private_data,
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:517:12:  [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 magic[2];
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:540:3:  [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 fext[1024];
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:541:3:  [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 buf[2048];
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:544:12:  [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 magic[2];
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:550:15:  [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).
  orig_file = fopen(fn, "rb");
data/caftools-2.0.3/src/libsrc/caf_read_scf.c:556:19:  [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).
      orig_file = fopen(fext, "rb");
data/caftools-2.0.3/src/libsrc/caf_types.h:69:8:  [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.
extern char *process_strings[process_types];
data/caftools-2.0.3/src/libsrc/caf_types.h:81:8:  [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.
extern char *pad_strings[pad_types];
data/caftools-2.0.3/src/libsrc/caf_types.h:93:8:  [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.
extern char *dye_strings[dye_types];
data/caftools-2.0.3/src/libsrc/caf_types.h:108:8:  [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.
extern char *primer_strings[primer_types];
data/caftools-2.0.3/src/libsrc/cafbin.c:98:3:  [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 buffer[1000];
data/caftools-2.0.3/src/libsrc/cafbin.c:246:3:  [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 buffer[10000];
data/caftools-2.0.3/src/libsrc/cafbin.c:405:3:  [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 buffer[10000];
data/caftools-2.0.3/src/libsrc/cafseq.c:186:4:  [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 class[128] ;
data/caftools-2.0.3/src/libsrc/cafseq.c:192:8:  [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 msg[256];
data/caftools-2.0.3/src/libsrc/cafseq.c:888:10:  [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 buf[1000][10];
data/caftools-2.0.3/src/libsrc/cafseq.c:890:10:  [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 buffer[10];
data/caftools-2.0.3/src/libsrc/cafseq.c:897:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(buf[j],"%d ", j);
data/caftools-2.0.3/src/libsrc/cafseq.c:904:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(buffer, "%d ", i);
data/caftools-2.0.3/src/libsrc/cafseq.c:915:3:  [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 buffer[1056], *s, *t;
data/caftools-2.0.3/src/libsrc/cafseq.c:956:3:  [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 buffer[1056], *s, *t;
data/caftools-2.0.3/src/libsrc/cafseq.c:957:3:  [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 tbuffer[1056];
data/caftools-2.0.3/src/libsrc/cafseq.c:968:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	  sprintf(tbuffer,"%d ",n); t = tbuffer;
data/caftools-2.0.3/src/libsrc/cafseq.c:1007:4:  [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(filename,"/dev/tty");
data/caftools-2.0.3/src/libsrc/cafseq.c:1024:3:  [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 filename[256];
data/caftools-2.0.3/src/libsrc/cafseq.c:1025:3:  [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(filename,"stdout");
data/caftools-2.0.3/src/libsrc/cafseq.c:1128:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			  memcpy(tag2,tag,sizeof(TAG));
data/caftools-2.0.3/src/libsrc/cafseq.c:1146:8:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	      memcpy(seq2,seq,sizeof(CAFSEQ));
data/caftools-2.0.3/src/libsrc/cafseq.c:1273:24:  [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).
      seq->staden_id = atoi(word);
data/caftools-2.0.3/src/libsrc/cafseq.c:1791:10:  [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 rawdata[266];
data/caftools-2.0.3/src/libsrc/cafseq.c:1792:3:  [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 arg[256];
data/caftools-2.0.3/src/libsrc/cafstrings.c:29:1:  [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 *sequence_text[sequence_types] = {   "Unknown_sequence",  "Is_read", "Is_contig", "Is_vector", "Is_group", "Is_assembly", "Is_spliced" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:31:1:  [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 *primer_strings[primer_types] = { "Unknown_primer", "Universal_primer", "Custom" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:32:1:  [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 *dye_strings[dye_types] = {"Unknown_dye", "Dye_primer", "Dye_terminator" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:33:1:  [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 *pad_strings[pad_types] = { "Unknown_state", "Padded", "Unpadded" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:34:1:  [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 *process_strings[process_types] = { "unknown", "PASS", "QUAL", "SVEC", "CVEC", "CONT" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:42:1:  [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 *status_text[status_count] = { "+", "replace", "insert", "delete", "unclear", "too_low", "masked_out", "unknown" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:44:1:  [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 *strand_text[strand_count] = { "none", "forward", "reverse" , "terminator", "", "double", "terminated", "forward_terminated", "reverse_terminated", "", "all_stranded" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:46:1:  [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 *Consensus_text[Consensus_count] = { "weak", "medium", "strong" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:48:1:  [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 *compound_text[compound_count] = { "isolated",  "compound" };
data/caftools-2.0.3/src/libsrc/cafstrings.c:50:1:  [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 *TAG_text[status_count] = { "YES", "REP", "INS", "DEL", "UNC", "LOW", "UNK" };
data/caftools-2.0.3/src/libsrc/cl.c:47:15:  [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 ( ( fp = fopen( make_legal(filename), mode ) ) == NULL )
data/caftools-2.0.3/src/libsrc/cl.c:64:3:  [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 Format[256];
data/caftools-2.0.3/src/libsrc/cl.c:66:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(Format,"%g",*variable);
data/caftools-2.0.3/src/libsrc/cl.c:119:10:  [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 stub[256];
data/caftools-2.0.3/src/libsrc/cl.c:136:3:  [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 Format[256];
data/caftools-2.0.3/src/libsrc/cl.c:138:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(Format,"%d",*variable);
data/caftools-2.0.3/src/libsrc/cl.c:204:7:  [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.
      char reply[256];
data/caftools-2.0.3/src/libsrc/cl.c:250:3:  [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 noformat[256];
data/caftools-2.0.3/src/libsrc/cl.c:297:3:  [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 Format[256];
data/caftools-2.0.3/src/libsrc/cl.c:339:14:  [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 ((fp = fopen( filename, "r" )) != 0)
data/caftools-2.0.3/src/libsrc/cl.c:451:5:  [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(pathname, "./");
data/caftools-2.0.3/src/libsrc/cl.c:477:3:  [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 name[512];
data/caftools-2.0.3/src/libsrc/cl.c:564:19:  [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 ( ( fp = fopen( filename, mode ) ) == NULL )
data/caftools-2.0.3/src/libsrc/cl.c:590:19:  [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 ( ( fp = fopen( filename, mode ) ) == NULL )
data/caftools-2.0.3/src/libsrc/cl.c:622:16:  [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).
  if ( ! (fp = fopen(filename,"r")) )
data/caftools-2.0.3/src/libsrc/cl.c:642:10:  [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 date[256];
data/caftools-2.0.3/src/libsrc/cl.c:647:14:  [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 ( (fp = fopen(filename,"r")) )
data/caftools-2.0.3/src/libsrc/cl.c:782:3:  [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 comfile[256], line[256], *s, **targv = argv;
data/caftools-2.0.3/src/libsrc/classify.c:974:3:  [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 filename[256];
data/caftools-2.0.3/src/libsrc/clipping.c:105:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/clipping.c:116:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(buf, "score %5d    match %5d mismatch %5d gap %5d\n", max_score, match, mismatch, gap );
data/caftools-2.0.3/src/libsrc/consensus.c:195:10:  [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 tab[256] = {0};
data/caftools-2.0.3/src/libsrc/dir.c:35:3:  [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 buf[1024];
data/caftools-2.0.3/src/libsrc/dir.c:55:67:  [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 ( matches_extension( fil->d_name, ext )  && (fp = (FILE*)fopen( buf, "r" ) ) ) /* && use_this_probe(fil->d_name) */
data/caftools-2.0.3/src/libsrc/dir.c:69:3:  [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 buf[256], *buf_ = buf;
data/caftools-2.0.3/src/libsrc/dir.c:104:67:  [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 ( matches_suffix( fil->d_name, suffix )  && (fp = (FILE*)fopen( buf, "r" ) ) ) /* && use_this_probe(fil->d_name) */
data/caftools-2.0.3/src/libsrc/lin_align.c:105:12:  [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 diagonal_path[4] = { 1, 4, 16, 64 };
data/caftools-2.0.3/src/libsrc/lin_align.c:106:12:  [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 delete_est_path[4] = { 2, 8, 32, 128 };
data/caftools-2.0.3/src/libsrc/lin_align.c:107:12:  [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 delete_genome_path[4] = { 3, 12, 48, 192 };
data/caftools-2.0.3/src/libsrc/lin_align.c:108:12:  [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 mask[4] = { 3, 12, 48, 192 };
data/caftools-2.0.3/src/libsrc/lin_align.c:960:3:  [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 format[256];
data/caftools-2.0.3/src/libsrc/lin_align.c:961:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(format, "%%%ds %%6d ", namelen );
data/caftools-2.0.3/src/libsrc/lin_align.c:1017:8:  [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 number[30];
data/caftools-2.0.3/src/libsrc/lin_align.c:1019:8:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	      sprintf(number," %d ", intron_width );
data/caftools-2.0.3/src/libsrc/lin_align.c:1131:5:  [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(sites->desc,"forward"); /* so that other functions know */
data/caftools-2.0.3/src/libsrc/lin_align.c:1141:5:  [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(sites->desc,"reverse"); /* so that other functions know */
data/caftools-2.0.3/src/libsrc/priority_queue.c:97:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(temp,item,pq->size);
data/caftools-2.0.3/src/libsrc/priority_queue.c:104:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(temp,item,pq->size);
data/caftools-2.0.3/src/libsrc/scf_cache.c:55:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/searchpath.c:44:14:  [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 ((fp = fopen(fullname,mode)) != 0)
data/caftools-2.0.3/src/libsrc/searchpath.c:54:12:  [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).
      fp = fopen(basename,mode);
data/caftools-2.0.3/src/libsrc/seq_dict.c:44:3:  [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 db[256];
data/caftools-2.0.3/src/libsrc/seq_dict.c:50:3:  [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  outfile[256];
data/caftools-2.0.3/src/libsrc/seq_dict.c:193:3:  [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 dictfile[256], name[256], buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:41:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:52:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:102:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:145:3:  [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 line[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:149:10:  [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 buf[MAX_BUF];
data/caftools-2.0.3/src/libsrc/seq_util.c:176:3:  [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 line[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:180:10:  [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 buf[MAX_BUF];
data/caftools-2.0.3/src/libsrc/seq_util.c:212:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:238:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:290:3:  [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 name[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:322:3:  [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 name[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:353:3:  [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 name[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:434:3:  [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 sname[256], line[512];
data/caftools-2.0.3/src/libsrc/seq_util.c:481:3:  [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 name[256], desc[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:548:3:  [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 sname[256], line[512];
data/caftools-2.0.3/src/libsrc/seq_util.c:593:3:  [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 sname[256], line[512];
data/caftools-2.0.3/src/libsrc/seq_util.c:670:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:672:3:  [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 sname[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:717:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:719:3:  [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 sname[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:765:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:767:3:  [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 name1[256], name2[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:857:10:  [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 *filenames[100];
data/caftools-2.0.3/src/libsrc/seq_util.c:890:3:  [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 line[256], seq[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:907:3:  [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 wild[256], line[256], name[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:926:3:  [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 buf[256], *sname, *db, *s;
data/caftools-2.0.3/src/libsrc/seq_util.c:956:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:972:3:  [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 wild[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:1208:10:  [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 *iub[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:1238:3:  [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 name[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:1239:3:  [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 desc[256];
data/caftools-2.0.3/src/libsrc/seq_util.c:1240:3:  [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 buf[MAXSEQLEN+1];
data/caftools-2.0.3/src/libsrc/sgrep.c:39:3:  [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 errbuf[256];
data/caftools-2.0.3/src/libsrc/trace_align.c:1597:3:  [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 mode[256];
data/caftools-2.0.3/src/libsrc/trace_align.c:1605:3:  [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(mode,"smith_waterman");
data/caftools-2.0.3/src/libsrc/trace_align.h:61:1:  [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 *align_modes[ALIGN_MODES] = { "smith_waterman", "needleman" };
data/caftools-2.0.3/src/libsrc/trace_align.h:63:8:  [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.
extern char *align_modes[ALIGN_MODES];
data/caftools-2.0.3/src/libsrc/tree_util.c:251:3:  [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 buf[256];
data/caftools-2.0.3/src/libsrc/tree_util.c:332:3:  [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 filename[256];
data/caftools-2.0.3/src/libsrc/wordhash.c:36:3:  [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 line[256];
data/caftools-2.0.3/src/libsrc/wordhash.c:37:3:  [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 word[245];
data/caftools-2.0.3/src/nd_clip.c:54:3:  [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 CAFfile[256];
data/caftools-2.0.3/src/nd_clip.c:55:3:  [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 clip_type[256];
data/caftools-2.0.3/src/nd_clip.c:66:3:  [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 logfile[256], outfile[256];
data/caftools-2.0.3/src/nd_edit.c:37:3:  [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 acefile[256];
data/caftools-2.0.3/src/nd_edit.c:38:3:  [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 outfile[256];
data/caftools-2.0.3/src/nd_edit.c:47:3:  [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(acefile,"stdin");
data/caftools-2.0.3/src/nd_edit.c:459:3:  [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 text[256];
data/caftools-2.0.3/src/ne_clip.c:38:3:  [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 CAFfile[256];
data/caftools-2.0.3/src/ne_clip.c:39:3:  [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 outfile[256];
data/caftools-2.0.3/src/ne_clip.c:43:3:  [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 logfile[256];
data/caftools-2.0.3/src/ne_clip.c:46:3:  [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 debug[256];
data/caftools-2.0.3/src/np_edit.c:50:3:  [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 CAFfile[256];
data/caftools-2.0.3/src/np_edit.c:51:3:  [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 outfile[256];
data/caftools-2.0.3/src/np_edit.c:55:3:  [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 logfile[256];
data/caftools-2.0.3/src/np_edit.c:86:3:  [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(outfile,"stdout");
data/caftools-2.0.3/src/phd2scf.c:187:12:  [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).
  fp_phd = fopen(phd_file, "r");
data/caftools-2.0.3/src/phd2scf.c:190:17:  [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).
  fp_trace_in = fopen(trace_file_in, "rb");
data/caftools-2.0.3/src/phd2scf.c:298:16:  [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).
  fp_scf_out = fopen(scf_file_out, "wb");
data/caftools-2.0.3/src/phd2scf.c:334:10:  [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 line[256];
data/caftools-2.0.3/src/phd2scf.c:335:10:  [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 discard[256];
data/caftools-2.0.3/src/phrapcons.c:25:3:  [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 caffile[256];
data/caftools-2.0.3/src/scf2phd.c:78:16:  [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).
      fp_scf = fopen(scf_file, "rb");
data/caftools-2.0.3/src/scf2phd.c:81:16:  [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).
      fp_phd = fopen(phd_file, "w");
data/caftools-2.0.3/src/scf2phd.c:148:3:  [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 line[1024];
data/caftools-2.0.3/src/scf2phd.c:149:3:  [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 phd[1024 + 6];
data/caftools-2.0.3/src/scf2phd.c:159:9:  [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(fofn, "r");
data/caftools-2.0.3/src/scf2phd.c:167:14:  [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).
    fp_scf = fopen(line, "rb");
data/caftools-2.0.3/src/scf2phd.c:171:5:  [2] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused). Risk is low because the
  source is a constant string.
    strcat(phd, ".phd.1");
data/caftools-2.0.3/src/scf2phd.c:173:14:  [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).
    fp_phd = fopen(phd, "w");
data/caftools-2.0.3/src/scf2phd.c:273:3:  [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 line[1024];
data/caftools-2.0.3/src/scf2phd.c:294:17:  [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).
  fp_phredpar = fopen(file, "r");
data/caftools-2.0.3/src/sdict.c:71:3:  [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 db[256], bufferfile[270], bufferfile2[550], bufferfile3[550], outfile[256], triple_file[270];
data/caftools-2.0.3/src/sdict.c:84:3:  [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 freqfile[256];
data/caftools-2.0.3/src/sdict.c:86:3:  [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 ignorefile[256];
data/caftools-2.0.3/src/sdict.c:90:3:  [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 tmpdir[256], mergefile[270];
data/caftools-2.0.3/src/sdict.c:118:7:  [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(outfile, "pairs");
data/caftools-2.0.3/src/sdict.c:128:3:  [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(tmpdir, "./");
data/caftools-2.0.3/src/sdict.c:307:13:  [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).
      bfp = fopen(bufferfile,"r");
data/caftools-2.0.3/src/sdict.c:317:15:  [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).
	      obfp = fopen(bufferfile2,"w");
data/caftools-2.0.3/src/sdict.c:335:15:  [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).
	      bfp1 = fopen(bufferfile2,"r");
data/caftools-2.0.3/src/sdict.c:339:15:  [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).
	      bfp2 = fopen(bufferfile3,"r");
data/caftools-2.0.3/src/sdict.c:344:15:  [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).
	      obfp = fopen(mergefile,"w");
data/caftools-2.0.3/src/sdict.c:385:13:  [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).
      bfp = fopen(bufferfile2,"r");
data/caftools-2.0.3/src/sdict.c:390:14:  [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).
      fclose(fopen(triple_file,"w")); /* create the file */
data/caftools-2.0.3/src/sdict.c:539:13:  [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).
      bfp = fopen( triple_file, "r" );
data/caftools-2.0.3/src/sdict.c:613:3:  [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 tmpfile[256];
data/caftools-2.0.3/src/sdict.c:613:8:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
  char tmpfile[256];
data/caftools-2.0.3/src/sdict.c:631:11:  [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).
  input = fopen(infile,"r"); /* open the existing file (which may be empty) */
data/caftools-2.0.3/src/sdict.c:632:10:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
  strcpy(tmpfile,tempnam(tmpdir,"sdict")); /* temp filename */
data/caftools-2.0.3/src/sdict.c:633:12:  [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).
  output = fopen(tmpfile,"w"); /* new file for merged data */
data/caftools-2.0.3/src/sdict.c:633:18:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
  output = fopen(tmpfile,"w"); /* new file for merged data */
data/caftools-2.0.3/src/sdict.c:688:10:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
  rename(tmpfile,infile);   /* swap the dump file names */
data/caftools-2.0.3/src/templates.c:59:3:  [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 caffile[1024] = {0};            /* CAF file to read    */
data/caftools-2.0.3/src/templates.c:62:3:  [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(caffile, "stdin");
data/caftools-2.0.3/src/templates.c:75:5:  [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(caffile, "stdin");
data/caftools-2.0.3/src/acedb/arraysub.c:642:19:  [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).
  while (s->ptr + strlen(text)  > s->safe) 
data/caftools-2.0.3/src/acedb/arraysub.c:643:20:  [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).
    stackExtend (s,strlen(text)+1) ;
data/caftools-2.0.3/src/acedb/arraysub.c:661:19:  [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).
  while (s->ptr + strlen(text) > s->safe)
data/caftools-2.0.3/src/acedb/arraysub.c:662:20:  [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).
    stackExtend (s,strlen(text)+1) ;
data/caftools-2.0.3/src/acedb/arraysub.c:697:7:  [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).
  n = strlen(delimiters) ;
data/caftools-2.0.3/src/acedb/arraysub.c:752:16:  [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 length = strlen (text) ;
data/caftools-2.0.3/src/acedb/filsubs.c:130:37:  [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).
    { fullpath = (char*) messalloc (strlen(dir) + 1) ;
data/caftools-2.0.3/src/acedb/filsubs.c:139:37:  [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).
      fullpath = (char*) messalloc (strlen(dir) + strlen(drive) + 1) ;
data/caftools-2.0.3/src/acedb/filsubs.c:139:51:  [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).
      fullpath = (char*) messalloc (strlen(dir) + strlen(drive) + 1) ;
data/caftools-2.0.3/src/acedb/filsubs.c:148:37:  [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).
    { fullpath = (char*) messalloc (strlen(pwd) + strlen(dir) + 2) ;
data/caftools-2.0.3/src/acedb/filsubs.c:148:51:  [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).
    { fullpath = (char*) messalloc (strlen(pwd) + strlen(dir) + 2) ;
data/caftools-2.0.3/src/acedb/filsubs.c:183:19:  [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).
      cp = name + strlen (name) ;
data/caftools-2.0.3/src/acedb/filsubs.c:423:14:  [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).
    endLen = strlen (ending) ;
data/caftools-2.0.3/src/acedb/filsubs.c:428:3:  [1] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused). Risk is low because the
  source is a constant character.
  strcat (entryPathName, "/") ;
data/caftools-2.0.3/src/acedb/filsubs.c:429:26:  [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).
  leaf = entryPathName + strlen(dirName) + 1 ;
data/caftools-2.0.3/src/acedb/filsubs.c:434:14:  [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).
      dLen = strlen (dName) ;
data/caftools-2.0.3/src/acedb/filsubs.c:485:7:  [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).
  if( strlen(path) >= 2  && 
data/caftools-2.0.3/src/acedb/filsubs.c:498:12:  [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).
	      if( strlen(cwd)+strlen(path)-1 > MAXPATHLEN )
data/caftools-2.0.3/src/acedb/filsubs.c:498:24:  [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).
	      if( strlen(cwd)+strlen(path)-1 > MAXPATHLEN )
data/caftools-2.0.3/src/acedb/filsubs.c:517:8:  [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).
	  if( strlen(cwd)+strlen(path)-1 > MAXPATHLEN ) /* Append relative path to cwd */
data/caftools-2.0.3/src/acedb/filsubs.c:517:20:  [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).
	  if( strlen(cwd)+strlen(path)-1 > MAXPATHLEN ) /* Append relative path to cwd */
data/caftools-2.0.3/src/acedb/freeout.c:156:8:  [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).
  ln = strlen(text) ;
data/caftools-2.0.3/src/acedb/freeout.c:238:7:  [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).
  if (strlen(outBuf) >= BUFSIZE)
data/caftools-2.0.3/src/acedb/freesubs.c:49:34:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
#define _FREECHAR     (currfil ? getc (currfil) : *currtext++)
data/caftools-2.0.3/src/acedb/freesubs.c:97:7:  [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).
  if (strlen(text) > 23)
data/caftools-2.0.3/src/acedb/freesubs.c:261:12:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  chint = getc(fil) ;
data/caftools-2.0.3/src/acedb/freesubs.c:272:14:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  if ((ch = getc (fil)) == '/')
data/caftools-2.0.3/src/acedb/freesubs.c:274:15:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	      while (getc(fil) != '\n' && !feof(fil)) {}
data/caftools-2.0.3/src/acedb/freesubs.c:285:10:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  *in = getc(fil) ;
data/caftools-2.0.3/src/acedb/freesubs.c:288:30:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	      while (isspace (*in = getc(fil))) ;    /* remove whitespace */
data/caftools-2.0.3/src/acedb/freesubs.c:723:16:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      answer = getchar () ;
data/caftools-2.0.3/src/acedb/freesubs.c:728:18:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        answer = getchar () ;
data/caftools-2.0.3/src/acedb/freesubs.c:889:27:  [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).
      array (a, base+3*(1+strlen(text)), char) = 0 ; /* ensure long enough */
data/caftools-2.0.3/src/acedb/freesubs.c:891:19:  [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).
      base += 1 + strlen(text) ;
data/caftools-2.0.3/src/acedb/freesubs.c:896:22:  [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).
      array (a, 2*(1+strlen(text)), char) = 0 ; /* ensure long enough */
data/caftools-2.0.3/src/acedb/freesubs.c:923:27:  [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).
      array (a, base+3*(1+strlen(text)), char) = 0 ; /* ensure long enough */
data/caftools-2.0.3/src/acedb/freesubs.c:925:19:  [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).
      base += 1 + strlen(text) ;
data/caftools-2.0.3/src/acedb/freesubs.c:930:22:  [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).
      array (a, 2*(1+strlen(text)), char) = 0 ; /* ensure long enough */
data/caftools-2.0.3/src/acedb/messubs.c:372:9:  [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).
	       strlen (messbuf)) ;
data/caftools-2.0.3/src/acedb/messubs.c:499:37:  [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).
    { result = (char *)halloc_dbg(1+strlen(old), handle, hfname, hlineno) ;
data/caftools-2.0.3/src/acedb/messubs.c:504:33:  [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).
    { result = (char *)halloc(1+strlen(old), handle);
data/caftools-2.0.3/src/acedb/timesubs.c:399:7:  [1] (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 character.
      strcpy (buf, "-") ;
data/caftools-2.0.3/src/caf2ace.c:17:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *read;  /* Read info            */
data/caftools-2.0.3/src/caf2ace.c:26:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/caf2ace.c:37:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/caf2ace.c:183:6:  [1] (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 character.
     strcpy(rinfo->comp,"C");
data/caftools-2.0.3/src/caf2ace.c:191:6:  [1] (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 character.
     strcpy(rinfo->comp,"U");
data/caftools-2.0.3/src/caf2ace.c:241:13:  [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 = strlen(s);
data/caftools-2.0.3/src/caf2ace.c:244:26:  [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).
    reverse_complement(s,strlen(s));
data/caftools-2.0.3/src/caf2ace.c:309:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  l = bs->read; 
data/caftools-2.0.3/src/caf2ace.c:316:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    l = bs->read;
data/caftools-2.0.3/src/caf2ace.c:329:64:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      fprintf(stdout,"AF %s %s %i\n",dictName(caf->seqDict,rp->read),rp->comp,(!strcmp(rp->comp,"C"))? rp->start : rp->start+1);
data/caftools-2.0.3/src/caf2ace.c:350:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      fprintf(stdout,"RD %s %i 0 0\n",dictName(caf->seqDict,rp->read),arrp(caf->seqs,rp->read,CAFSEQ)->len);
data/caftools-2.0.3/src/caf2ace.c:350:90:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      fprintf(stdout,"RD %s %i 0 0\n",dictName(caf->seqDict,rp->read),arrp(caf->seqs,rp->read,CAFSEQ)->len);
data/caftools-2.0.3/src/caf2ace.c:351:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      cseq = arrp(caf->seqs,rp->read,CAFSEQ);
data/caftools-2.0.3/src/caf2ace.c:354:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      write_chromat(caf,cseq,rp->read,reads,i,t_string);
data/caftools-2.0.3/src/caf2ace.c:361:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
static int write_chromat (cafAssembly *caf, CAFSEQ *read, int read_id, Array reads, int pos, char *t_string) 
data/caftools-2.0.3/src/caf2ace.c:397:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cread = bp->read;  
data/caftools-2.0.3/src/caf2ace.c:409:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    cread = bp->read;
data/caftools-2.0.3/src/caf2ace.c:503:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bp->read = (se->read)->id;
data/caftools-2.0.3/src/caf2ace.c:507:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bp->read = (se->read)->id;
data/caftools-2.0.3/src/caf2fastq.c:143:15:  [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).
      right = strlen(dna);
data/caftools-2.0.3/src/caf2gap.c:612:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            CAFSEQ    *read;
data/caftools-2.0.3/src/caf2gap.c:1117:40:  [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).
  return write_string_len(gap_db, str, strlen(str));
data/caftools-2.0.3/src/caf2gap.c:1210:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(converted_dna, dna, len);
data/caftools-2.0.3/src/caf2gap.c:1414:17:  [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 = min(strlen(s), sizeof(GCardinal));
data/caftools-2.0.3/src/caf2gap.c:1479:10:  [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).
	       (strlen(tag_type)
data/caftools-2.0.3/src/caf2gap.c:1480:20:  [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).
		+ (tag_comment ? strlen(tag_comment) : 0)
data/caftools-2.0.3/src/caf2gap.c:1845:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  GReadings read;
data/caftools-2.0.3/src/caf2gap.c:1880:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.name = write_string(gap_db, read_name);
data/caftools-2.0.3/src/caf2gap.c:1882:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.trace_name = write_string(gap_db, read_seq->SCF_File);
data/caftools-2.0.3/src/caf2gap.c:1883:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.trace_type = write_string(gap_db, "ANY");
data/caftools-2.0.3/src/caf2gap.c:1885:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.trace_name = 0;
data/caftools-2.0.3/src/caf2gap.c:1886:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.trace_type = 0;
data/caftools-2.0.3/src/caf2gap.c:1889:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.left  = last_read;
data/caftools-2.0.3/src/caf2gap.c:1890:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.right = next_read;
data/caftools-2.0.3/src/caf2gap.c:1891:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.position = read_pos;
data/caftools-2.0.3/src/caf2gap.c:1892:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.length = read_seq->len;
data/caftools-2.0.3/src/caf2gap.c:1893:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.sense  = read_sense;
data/caftools-2.0.3/src/caf2gap.c:1894:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.sequence = write_sequence(gap_db, read_seq->dna, read_sense,
data/caftools-2.0.3/src/caf2gap.c:1895:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				 read.length);
data/caftools-2.0.3/src/caf2gap.c:1902:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.confidence = write_confidence(gap_db, read_seq->base_quality,
data/caftools-2.0.3/src/caf2gap.c:1903:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				     read_sense, read.length);
data/caftools-2.0.3/src/caf2gap.c:1905:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.orig_positions = write_positions(gap_db, read_seq->assinf, read_sense,
data/caftools-2.0.3/src/caf2gap.c:1906:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					  read.length);
data/caftools-2.0.3/src/caf2gap.c:1909:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.orig_positions = write_positions_pads(gap_db, read_seq->dna,
data/caftools-2.0.3/src/caf2gap.c:1913:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.orig_positions = write_positions_pads(gap_db, read_seq->dna,
data/caftools-2.0.3/src/caf2gap.c:1914:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					       read_sense, read.length);
data/caftools-2.0.3/src/caf2gap.c:1916:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.chemistry = read_seq->dye == dye_terminator ? 1 : 0;
data/caftools-2.0.3/src/caf2gap.c:1917:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.annotations = process_tags(gap_db, caf, read_seq, map,
data/caftools-2.0.3/src/caf2gap.c:1918:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				  1, read.length, 0);
data/caftools-2.0.3/src/caf2gap.c:1920:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.notes = process_notes(gap_db, caf, read_seq, map,
data/caftools-2.0.3/src/caf2gap.c:1923:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.sequence_length = af->r2 - af->r1 + 1;
data/caftools-2.0.3/src/caf2gap.c:1924:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.start = read_start;
data/caftools-2.0.3/src/caf2gap.c:1925:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.end   = read_end;
data/caftools-2.0.3/src/caf2gap.c:1926:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.template = process_template(gap_db, caf, read_seq, map);
data/caftools-2.0.3/src/caf2gap.c:1927:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.strand = (read_seq->strand == reverse_strand
data/caftools-2.0.3/src/caf2gap.c:1931:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.primer = (read_seq->strand == reverse_strand
data/caftools-2.0.3/src/caf2gap.c:1934:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.primer = (read_seq->strand == reverse_strand
data/caftools-2.0.3/src/caf2gap.c:1938:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read.primer = (read_seq->primer == custom_primer
data/caftools-2.0.3/src/caf2gap.c:1948:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  rr = write_record(gap_db, GR_NEW, GT_Readings, &read,
data/caftools-2.0.3/src/caf2gap.c:2251:3:  [1] (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 character.
  strcpy(version,"0");
data/caftools-2.0.3/src/caf2phrap.c:84:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  char read[256];
data/caftools-2.0.3/src/caf2phrap.c:153:3:  [1] (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 character.
  strcpy(tag_mask, "");
data/caftools-2.0.3/src/caf2phrap.c:157:3:  [1] (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 character.
  strcpy(mask_text, "x");
data/caftools-2.0.3/src/caf2phrap.c:252:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		  sscanf(line, "%s", read );
data/caftools-2.0.3/src/caf2phrap.c:253:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		  readname = file_part(read);
data/caftools-2.0.3/src/caf2phrap.c:372:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/caf2phrap.c:657:11:  [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).
    len = strlen(path);
data/caftools-2.0.3/src/caf_check_pads.h:9:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *read;  /* Read info            */
data/caftools-2.0.3/src/caf_check_pads.h:18:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/cafcat.c:108:12:  [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).
					len = strlen(dna);
data/caftools-2.0.3/src/cafcat.c:132:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			char read[256];
data/caftools-2.0.3/src/cafcat.c:149:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				sscanf(line, "%s", read);
data/caftools-2.0.3/src/cafcat.c:150:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				readname = file_part(read);
data/caftools-2.0.3/src/cafcat.c:238:11:  [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).
    len = strlen(path);
data/caftools-2.0.3/src/libsrc/assembly.c:988:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/libsrc/auto_edit.h:269:112:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
void propose_clip_alignment( contigAlignment *Align, cafAssembly *CAF, int extend, FILE *logf , int match, int mismatch, int gap, int neutral, char *debug, int original );
data/caftools-2.0.3/src/libsrc/banded.c:32:65:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
bandedAlignment( SEQUENCE *seq1, SEQUENCE *seq2, int match, int mismatch, int gap, int neutral, int window )
data/caftools-2.0.3/src/libsrc/banded.c:61:8:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if ( mismatch > 0 )
data/caftools-2.0.3/src/libsrc/banded.c:62:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    mismatch = -mismatch;
data/caftools-2.0.3/src/libsrc/banded.c:66:81:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  as = smith_waterman_alignment2(seq1->s, seq2->s, seq1->len, seq2->len, match, mismatch, gap, neutral, diagonal, window);
data/caftools-2.0.3/src/libsrc/base_edit.c:222:14:  [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).
	      len = strlen(dna);
data/caftools-2.0.3/src/libsrc/base_edit.c:448:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/libsrc/caf.h:139:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;       /* the id of the read affected by the edit */
data/caftools-2.0.3/src/libsrc/caf_check.c:176:15:  [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).
	  seq->len = strlen(stackText(seq->dna,0));
data/caftools-2.0.3/src/libsrc/caf_check.c:383:13:  [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).
	seq->len = strlen(stackText(seq->dna,0));
data/caftools-2.0.3/src/libsrc/caf_check.c:636:12:  [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).
	    len = strlen(stackText(contig->dna,0));
data/caftools-2.0.3/src/libsrc/cafbin.c:69:13:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if ( (c = getc( fil )) != '#' ) 
data/caftools-2.0.3/src/libsrc/cafbin.c:108:14:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  while( (c=getc(fp)) && c != EOF ) 
data/caftools-2.0.3/src/libsrc/cafbin.c:174:13:  [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).
      len = strlen(dna)+1;
data/caftools-2.0.3/src/libsrc/cafbin.c:229:13:  [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).
      len = strlen(other)+1;
data/caftools-2.0.3/src/libsrc/cafbin.c:238:27:  [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).
    fwrite(s,sizeof(char),strlen(s)+1,fp);
data/caftools-2.0.3/src/libsrc/cafbin.c:251:12:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while((c=getc(fp)) && c != EOF)
data/caftools-2.0.3/src/libsrc/cafbin.c:256:9:  [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).
  len = strlen(buffer);
data/caftools-2.0.3/src/libsrc/cafbin.c:294:10:  [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).
	  len = strlen(dna);
data/caftools-2.0.3/src/libsrc/cafbin.c:367:10:  [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).
	  len = strlen(other);
data/caftools-2.0.3/src/libsrc/cafbin.c:391:36:  [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).
	    fwrite(tag->text,sizeof(char),strlen(tag->text)+1,fp);
data/caftools-2.0.3/src/libsrc/cafbin.c:420:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  while((*s++=getc(fp)));
data/caftools-2.0.3/src/libsrc/cafbin.c:421:10:  [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).
	  len = strlen(buffer);
data/caftools-2.0.3/src/libsrc/cafseq.c:444:17:  [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 = strlen(s);
data/caftools-2.0.3/src/libsrc/cafseq.c:1335:14:  [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).
  seq->len = strlen(stackText(seq->dna,0));
data/caftools-2.0.3/src/libsrc/cafseq.c:1348:11:  [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).
    len = strlen(stackText(seq->dna,0))+2;
data/caftools-2.0.3/src/libsrc/cafseq.c:1370:11:  [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).
    len = strlen(stackText(seq->dna,0))+2;
data/caftools-2.0.3/src/libsrc/cafseq.c:1693:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/libsrc/cl.c:342:24:  [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).
	      for(i =0 ; i <= strlen(argv[argc]); i++)
data/caftools-2.0.3/src/libsrc/cl.c:385:7:  [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).
  n = strlen(filename);
data/caftools-2.0.3/src/libsrc/cl.c:392:11:  [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).
      n = strlen(filename);
data/caftools-2.0.3/src/libsrc/cl.c:400:19:  [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).
  if ( filename[n=strlen(filename)-1] == '.' )
data/caftools-2.0.3/src/libsrc/cl.c:425:7:  [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).
  n = strlen(filename);
data/caftools-2.0.3/src/libsrc/cl.c:445:23:  [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).
  char *s = &pathname[strlen(pathname)-1];
data/caftools-2.0.3/src/libsrc/cl.c:453:5:  [1] (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 character.
    strcpy(pathname,"/");
data/caftools-2.0.3/src/libsrc/cl.c:483:16:  [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).
      if ( dir[strlen(dir)-1] != '/' )
data/caftools-2.0.3/src/libsrc/cl.c:645:3:  [1] (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 character.
  strcpy( date, "?");
data/caftools-2.0.3/src/libsrc/cl.c:750:9:  [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).
	  if ( strlen(arg) > 3  && (arg[1] == 'n') && (arg[2] == 'o') )
data/caftools-2.0.3/src/libsrc/cl.c:756:48:  [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).
	  while( u && strncmp( argv[argc], u->format, strlen(argv[argc]) ) && ( noarg == NULL || strncmp( noarg, &u->format[1], strlen(noarg) ) ) )
data/caftools-2.0.3/src/libsrc/cl.c:756:122:  [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).
	  while( u && strncmp( argv[argc], u->format, strlen(argv[argc]) ) && ( noarg == NULL || strncmp( noarg, &u->format[1], strlen(noarg) ) ) )
data/caftools-2.0.3/src/libsrc/cl.c:801:44:  [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).
	  if ( argv[n] && strncmp( COM, argv[n] , strlen(COM) ) )
data/caftools-2.0.3/src/libsrc/cl.c:882:8:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	      strncpy(item[*items],t,len);
data/caftools-2.0.3/src/libsrc/clipping.c:66:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
rescore_alignment( CAFSEQ *read, ASSINF *lax, contigAlignment *Align, int original, int match, int mismatch, int gap, int *clip_left_at, int *clip_right_at, int *lax_score, int *strict_score );
data/caftools-2.0.3/src/libsrc/clipping.c:66:100:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
rescore_alignment( CAFSEQ *read, ASSINF *lax, contigAlignment *Align, int original, int match, int mismatch, int gap, int *clip_left_at, int *clip_right_at, int *lax_score, int *strict_score );
data/caftools-2.0.3/src/libsrc/clipping.c:92:92:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
generate_clip_points( contigAlignment *Align, cafAssembly *CAF, FILE *logf, int match, int mismatch, int gap, int neutral, char *debug_read, int original, char *tagType )
data/caftools-2.0.3/src/libsrc/clipping.c:107:18:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  mat_init(match,mismatch,gap,neutral,padding_char); /* initialise the matrix for matching sybmbols */
data/caftools-2.0.3/src/libsrc/clipping.c:114:58:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      rescore_alignment( seq, a, Align, original, match, mismatch, gap, &x1, &x2, &lax_s, &max_score);
data/caftools-2.0.3/src/libsrc/clipping.c:116:87:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      sprintf(buf, "score %5d    match %5d mismatch %5d gap %5d\n", max_score, match, mismatch, gap );
data/caftools-2.0.3/src/libsrc/clipping.c:127:106:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
propose_clip_alignment( contigAlignment *Align, cafAssembly *CAF, int extend, FILE *logf, int match, int mismatch, int gap, int neutral, char *debug_read, int original )
data/caftools-2.0.3/src/libsrc/clipping.c:194:18:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  mat_init(match,mismatch,gap,neutral,padding_char); /* initialise the matrix for matching sybmbols */
data/caftools-2.0.3/src/libsrc/clipping.c:272:55:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	rescore_alignment( seq, lax, Align, original, match, mismatch, gap, &strict->r1, &strict->r2, &lax_s, &max_score);
data/caftools-2.0.3/src/libsrc/clipping.c:791:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
rescore_alignment( CAFSEQ *read, ASSINF *lax, contigAlignment *Align, int original, int match, int mismatch, int gap, int *clip_left_at, int *clip_right_at, int *lax_score, int *strict_score )
data/caftools-2.0.3/src/libsrc/clipping.c:791:100:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
rescore_alignment( CAFSEQ *read, ASSINF *lax, contigAlignment *Align, int original, int match, int mismatch, int gap, int *clip_left_at, int *clip_right_at, int *lax_score, int *strict_score )
data/caftools-2.0.3/src/libsrc/cmp.c:75:12:  [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 la = strlen(a)-1;
data/caftools-2.0.3/src/libsrc/cmp.c:76:12:  [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 lb = strlen(b)-1;
data/caftools-2.0.3/src/libsrc/consensus.c:19:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *read;  /* Read info            */
data/caftools-2.0.3/src/libsrc/dir.c:71:20:  [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).
  size_t dir_len = strlen(dir);
data/caftools-2.0.3/src/libsrc/dir.c:90:26:  [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).
      size_t fname_len = strlen(fil->d_name);
data/caftools-2.0.3/src/libsrc/dir.c:120:13:  [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 pos = strlen(name)-strlen(suffix);
data/caftools-2.0.3/src/libsrc/dir.c:120:26:  [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 pos = strlen(name)-strlen(suffix);
data/caftools-2.0.3/src/libsrc/lin_align.c:56:78:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
non_recursive_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, int backtrack, int needleman, int init_path )
data/caftools-2.0.3/src/libsrc/lin_align.c:479:74:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
recursive_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, float max_area, int init_path )
data/caftools-2.0.3/src/libsrc/lin_align.c:496:61:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      ge = non_recursive_est_to_genome( est, genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, splice_sites, 1, 1, DIAGONAL );
data/caftools-2.0.3/src/libsrc/lin_align.c:512:52:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  score = midpt_est_to_genome( est, genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, splice_sites, middle, &gleft, &gright );
data/caftools-2.0.3/src/libsrc/lin_align.c:535:68:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  left_ge = recursive_est_to_genome( left_est, left_genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, left_splice, max_area, DIAGONAL );  
data/caftools-2.0.3/src/libsrc/lin_align.c:538:71:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  right_ge = recursive_est_to_genome( right_est, right_genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, right_splice, max_area, DIAGONAL );  
data/caftools-2.0.3/src/libsrc/lin_align.c:579:77:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
linear_space_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, float megabytes )
data/caftools-2.0.3/src/libsrc/lin_align.c:592:63:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      return non_recursive_est_to_genome( est, genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, splice_sites, 1, 0, DIAGONAL );
data/caftools-2.0.3/src/libsrc/lin_align.c:598:61:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      ge = non_recursive_est_to_genome( est, genome, match, mismatch, gap_penalty, intron_penalty, splice_penalty, splice_sites, 0, 0, DIAGONAL );  
data/caftools-2.0.3/src/libsrc/lin_align.c:612:72:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      rge = recursive_est_to_genome( est_subseq, genome_subseq, match, mismatch, gap_penalty, intron_penalty, splice_penalty, splice_subseq, max_area, DIAGONAL );  
data/caftools-2.0.3/src/libsrc/lin_align.c:629:70:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
midpt_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, int middle, int *gleft, int *gright )
data/caftools-2.0.3/src/libsrc/lin_align.c:824:100:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
blast_style_output( FILE *blast, SEQUENCE *genome, SEQUENCE *est, ge_alignment *ge, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, int gapped, int reverse  )
data/caftools-2.0.3/src/libsrc/lin_align.c:959:17:  [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 namelen = strlen(genome->name) > strlen(est->name) ? strlen(genome->name): strlen(est->name)  ;
data/caftools-2.0.3/src/libsrc/lin_align.c:959:40:  [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 namelen = strlen(genome->name) > strlen(est->name) ? strlen(genome->name): strlen(est->name)  ;
data/caftools-2.0.3/src/libsrc/lin_align.c:959:60:  [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 namelen = strlen(genome->name) > strlen(est->name) ? strlen(genome->name): strlen(est->name)  ;
data/caftools-2.0.3/src/libsrc/lin_align.c:959:82:  [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 namelen = strlen(genome->name) > strlen(est->name) ? strlen(genome->name): strlen(est->name)  ;
data/caftools-2.0.3/src/libsrc/lin_align.c:1020:17:  [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).
	      numlen = strlen(number);
data/caftools-2.0.3/src/libsrc/lin_align.c:1148:24:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
matinit(int match, int mismatch, int gap, int neutral, char padding_char)
data/caftools-2.0.3/src/libsrc/lin_align.c:1169:45:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	      lsimmat[c1][c2] = lsimmat[c2][c1] = -mismatch;
data/caftools-2.0.3/src/libsrc/lin_align.h:62:100:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
blast_style_output( FILE *blast, SEQUENCE *genome, SEQUENCE *est, ge_alignment *ge, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, int gapped, int reverse  );
data/caftools-2.0.3/src/libsrc/lin_align.h:68:77:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
linear_space_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, float max_area );
data/caftools-2.0.3/src/libsrc/lin_align.h:71:74:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
recursive_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, float max_area, int init_path );
data/caftools-2.0.3/src/libsrc/lin_align.h:74:78:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
non_recursive_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, int backtrack, int needleman, int init_path );
data/caftools-2.0.3/src/libsrc/lin_align.h:77:70:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
midpt_est_to_genome( SEQUENCE *est, SEQUENCE *genome, int match, int mismatch, int gap_penalty, int intron_penalty, int splice_penalty, SEQUENCE *splice_sites, int middle, int *gleft, int *gright );
data/caftools-2.0.3/src/libsrc/lin_align.h:83:24:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
matinit(int match, int mismatch, int gap, int neutral, char pad_char);
data/caftools-2.0.3/src/libsrc/padding.c:213:27:  [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).
    unpadded_contig_len = strlen(unpadded_contig_dna);
data/caftools-2.0.3/src/libsrc/padding.c:344:23:  [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).
	  unpadded_dna_len = strlen(unpadded_dna);
data/caftools-2.0.3/src/libsrc/padding.c:396:18:  [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 slen = strlen(old);
data/caftools-2.0.3/src/libsrc/padding.c:424:14:  [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).
  seq->len = strlen(stackText(new_dna,0));
data/caftools-2.0.3/src/libsrc/padding.c:773:12:  [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).
	  c_len = strlen(c_dna+1);
data/caftools-2.0.3/src/libsrc/padding.c:793:13:  [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).
		  r_len = strlen(r_dna+1);
data/caftools-2.0.3/src/libsrc/padding.c:926:16:  [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).
		  seq->len = strlen(r_dna+1);
data/caftools-2.0.3/src/libsrc/padding.c:937:18:  [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).
	  contig->len = strlen(c_dna+1);
data/caftools-2.0.3/src/libsrc/padding.c:940:32:  [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).
	  adjust_quality(contig,c_map,strlen(c_dna+1),0);
data/caftools-2.0.3/src/libsrc/padding.c:1148:15:  [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).
      r_len = strlen(r_dna+1);
data/caftools-2.0.3/src/libsrc/padding.c:1164:18:  [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).
      seq->len = strlen(r_dna+1);
data/caftools-2.0.3/src/libsrc/readline.c:34:15:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((c = getc(file)) != EOF)  {
data/caftools-2.0.3/src/libsrc/readline.c:47:15:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((c = getc(file)) != EOF) {
data/caftools-2.0.3/src/libsrc/seq_dict.c:35:21:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			  int match, int mismatch,
data/caftools-2.0.3/src/libsrc/seq_util.c:163:9:  [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).
	  if ( strlen(buf) + strlen(line) + 2 < MAX_BUF )
data/caftools-2.0.3/src/libsrc/seq_util.c:163:23:  [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).
	  if ( strlen(buf) + strlen(line) + 2 < MAX_BUF )
data/caftools-2.0.3/src/libsrc/seq_util.c:164:36:  [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).
	    strcat( buf, clean_line(line)+strlen(key) );
data/caftools-2.0.3/src/libsrc/seq_util.c:198:13:  [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).
	      if ( strlen(buf) + strlen(line) + 2 < MAX_BUF )
data/caftools-2.0.3/src/libsrc/seq_util.c:198:27:  [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).
	      if ( strlen(buf) + strlen(line) + 2 < MAX_BUF )
data/caftools-2.0.3/src/libsrc/seq_util.c:199:33:  [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).
		strcat( buf, clean_line(line)+strlen(key) );
data/caftools-2.0.3/src/libsrc/seq_util.c:467:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (c = getc(database->datafile)) != '/' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:492:13:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while( (c=getc(fp)) != '>' && c != EOF );
data/caftools-2.0.3/src/libsrc/seq_util.c:501:26:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      while( ! isspace(c=getc(fp)) ) 
data/caftools-2.0.3/src/libsrc/seq_util.c:509:49:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      while( c != '\n' && c != EOF && isspace(c=getc(fp)) );
data/caftools-2.0.3/src/libsrc/seq_util.c:516:8:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  c = getc(fp);
data/caftools-2.0.3/src/libsrc/seq_util.c:522:17:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      while( (c=getc(fp)) != '>' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:574:12:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while((c=getc(database->datafile)) != '>' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:582:13:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while( (c=getc(database->datafile)) != '>' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:620:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (c = getc(database->datafile)) != '>' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:631:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (c = getc(database->datafile)) != '>' && c != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:645:34:  [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).
      if ( !strncmp( line, text, strlen(text) ) )
data/caftools-2.0.3/src/libsrc/seq_util.c:646:19:  [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).
	return ftell(fp)-strlen(line);
data/caftools-2.0.3/src/libsrc/seq_util.c:685:16:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (c = fgetc( datafile ) ) != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:732:16:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (c = fgetc( datafile ) ) != EOF )
data/caftools-2.0.3/src/libsrc/seq_util.c:812:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = getc(fp);
data/caftools-2.0.3/src/libsrc/seq_util.c:828:9:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		  c = getc(fp);
data/caftools-2.0.3/src/libsrc/seq_util.c:909:13:  [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 = strlen(wild);
data/caftools-2.0.3/src/libsrc/seq_util.c:1156:11:  [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=strlen(iubstring);
data/caftools-2.0.3/src/libsrc/seq_util.c:1162:14:  [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).
      len += strlen(t);
data/caftools-2.0.3/src/libsrc/seq_util.c:1186:11:  [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).
	  len += strlen(s);
data/caftools-2.0.3/src/libsrc/seq_util.c:1309:14:  [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).
  seq->len = strlen(s);
data/caftools-2.0.3/src/libsrc/seq_util.c:1331:16:  [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).
  size_t len = strlen(s);
data/caftools-2.0.3/src/libsrc/sw.c:34:22:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			   int match, int mismatch, int gap, int neutral,
data/caftools-2.0.3/src/libsrc/sw.c:38:74:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
int smith_waterman_score( SEQUENCE *seq1, SEQUENCE *seq2, int match, int mismatch, int gap, int neutral, int offset, int window, int *coord1, int *coord2 )
data/caftools-2.0.3/src/libsrc/sw.c:45:75:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  alignStruct *as = smith_waterman_alignment2( s1, s2, len1, len2, match, mismatch, gap, neutral, offset, window );
data/caftools-2.0.3/src/libsrc/sw.c:46:65:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  int score = smith_waterman_score2( s1, s2, len1, len2, match, mismatch, gap, neutral, offset, window, coord1, coord2);
data/caftools-2.0.3/src/libsrc/sw.c:53:83:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
int smith_waterman_score2( char *s1, char *s2, int len1, int len2, int match, int mismatch, int gap, int neutral, int offset, int window,  int *end_coord1, int *end_coord2 )
data/caftools-2.0.3/src/libsrc/sw.c:74:20:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    mat_init(match,mismatch,gap,neutral,pad_char);
data/caftools-2.0.3/src/libsrc/sw.c:76:18:  [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).
  if ( len1 > (m=strlen(s1)) )
data/caftools-2.0.3/src/libsrc/sw.c:79:18:  [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).
  if ( len2 > (m=strlen(s2)) )
data/caftools-2.0.3/src/libsrc/sw.c:175:83:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
smith_waterman_alignment2( char *s1, char *s2, int len1, int len2, int match, int mismatch, int gap, int neutral, int offset, int window )
data/caftools-2.0.3/src/libsrc/sw.c:201:20:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    mat_init(match,mismatch,gap, neutral, pad_char);
data/caftools-2.0.3/src/libsrc/sw.c:203:18:  [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).
  if ( len1 > (m=strlen(s1)) )
data/caftools-2.0.3/src/libsrc/sw.c:206:18:  [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).
  if ( len2 > (m=strlen(s2)) )
data/caftools-2.0.3/src/libsrc/sw.c:419:50:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
equivalent_bases( int c1, int c2, int match, int mismatch, int gap )
data/caftools-2.0.3/src/libsrc/sw.c:435:9:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	return mismatch;
data/caftools-2.0.3/src/libsrc/sw.c:440:25:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
mat_init(int match, int mismatch, int gap, int neutral, char pad_char)
data/caftools-2.0.3/src/libsrc/sw.c:462:44:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	      sim_mat[c1][c2] = sim_mat[c2][c1] = mismatch;
data/caftools-2.0.3/src/libsrc/sw.h:46:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/libsrc/sw.h:72:96:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
alignStruct *smith_waterman_alignment2( char *s1, char *s2, int len1, int len2, int match, int mismatch, int gap, int neutral, int offset, int window );
data/caftools-2.0.3/src/libsrc/sw.h:73:54:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
int equivalent_bases( int c1, int c2, int match, int mismatch, int gap );
data/caftools-2.0.3/src/libsrc/sw.h:74:30:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
void mat_init(int match, int mismatch, int gap, int neutral, char padding_char );
data/caftools-2.0.3/src/libsrc/sw.h:80:92:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
alignStruct *reAlign2( char *paddedConsensus, Array mapping, sw_struct *sw, int match, int mismatch, int gap, int window );
data/caftools-2.0.3/src/libsrc/sw.h:81:48:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
Array reAlign( Collation *coll, int match, int mismatch, int gap, int window );
data/caftools-2.0.3/src/libsrc/sw.h:83:78:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
alignStruct *bandedAlignment( SEQUENCE *seq1, SEQUENCE *seq2, int match, int mismatch, int gap, int neutral, int window );
data/caftools-2.0.3/src/libsrc/trace_quality.c:389:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
get_trace_quality( cafAssembly *Ass, int read, int strand, int coord, traceQuality *tq, int base )
data/caftools-2.0.3/src/libsrc/trace_quality.c:393:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *seq = arrp(Ass->seqs,read,CAFSEQ);
data/caftools-2.0.3/src/libsrc/trace_quality.c:812:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
possible_overcall( cafAssembly *Ass, int read, int strand, int coord, int direction, int base)
data/caftools-2.0.3/src/libsrc/trace_quality.c:823:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *seq = arrp(Ass->seqs,read,CAFSEQ); 
data/caftools-2.0.3/src/libsrc/trace_quality.c:976:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
peak_count( cafAssembly *Ass, int read, int strand, int coord, int direction, int base, int range, int min_width)
data/caftools-2.0.3/src/libsrc/trace_quality.c:981:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *seq = arrp(Ass->seqs,read,CAFSEQ);
data/caftools-2.0.3/src/libsrc/trace_quality.c:1236:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
accumulate_votes( cafAssembly *Ass, int read, int strand, int tcoord, float *votes )
data/caftools-2.0.3/src/libsrc/trace_quality.c:1239:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *seq = arrp(Ass->seqs,read,CAFSEQ);
data/caftools-2.0.3/src/libsrc/trace_quality.c:1314:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/libsrc/trace_quality.c:1321:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if ( read < 0 )
data/caftools-2.0.3/src/libsrc/trace_quality.c:1484:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
isolated_peak( cafAssembly *Ass, int read, int strand, int coord, char base )
data/caftools-2.0.3/src/libsrc/trace_quality.c:1487:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *seq = arrp(Ass->seqs,read,CAFSEQ);
data/caftools-2.0.3/src/libsrc/trace_quality.c:1757:43:  [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).
	      seq->SCF_File = (char*)messalloc(1+strlen(dictName(Ass->seqDict,seq->id) ) );
data/caftools-2.0.3/src/libsrc/trace_quality.h:13:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int  get_trace_quality(cafAssembly *Ass, int read, int strand, int coord,
data/caftools-2.0.3/src/libsrc/trace_quality.h:40:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int possible_overcall(cafAssembly *Ass, int read, int strand, int coord,
data/caftools-2.0.3/src/libsrc/trace_quality.h:46:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int peak_count(cafAssembly *Ass, int read, int strand, int coord,
data/caftools-2.0.3/src/libsrc/trace_quality.h:54:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void accumulate_votes( cafAssembly *Ass, int read, int strand, int tcoord,
data/caftools-2.0.3/src/libsrc/trace_quality.h:83:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int isolated_peak( cafAssembly *Ass, int read, int strand, int coord,
data/caftools-2.0.3/src/libsrc/wordhash.c:48:15:  [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).
	  Wordsize = strlen(word);
data/caftools-2.0.3/src/nd_clip.c:68:3:  [1] (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 character.
  strcpy(clip_type,"");
data/caftools-2.0.3/src/nd_edit.c:116:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/nd_edit.c:259:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		      a->seq = read;
data/caftools-2.0.3/src/nd_edit.c:283:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	      a->seq = read;
data/caftools-2.0.3/src/nd_edit.c:320:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/caftools-2.0.3/src/nd_edit.c:326:13:  [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).
      len = strlen(dna);
data/caftools-2.0.3/src/ne_clip.c:58:23:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  getint("-mismatch",&mismatch,argc,argv);
data/caftools-2.0.3/src/ne_clip.c:65:8:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if ( mismatch > 0 )
data/caftools-2.0.3/src/ne_clip.c:66:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    mismatch = -mismatch;
data/caftools-2.0.3/src/ne_clip.c:117:68:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		  propose_clip_alignment( Alignment, CAF, extend, log_fp, match, mismatch, gap, neutral, debug, original );
data/caftools-2.0.3/src/phd2scf.c:74:17:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = getchar()) != EOF) {
data/caftools-2.0.3/src/phrapcons.c:123:71:  [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).
      len = ( contig->base_quality ? arrayMax(contig->base_quality) : strlen(contig_dna)+2 );
data/caftools-2.0.3/src/phrapcons.c:206:10:  [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).
	  len = strlen(contig_dna+1);
data/caftools-2.0.3/src/scf2phd.c:46:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
static void get_chem_info(Read *read, char **chem, char **dye,
data/caftools-2.0.3/src/scf2phd.c:213:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (!read) return 1;
data/caftools-2.0.3/src/scf2phd.c:215:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  get_chem_info(read, &chem, &dye, chem_list);
data/caftools-2.0.3/src/scf2phd.c:263:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  read_deallocate(read);
data/caftools-2.0.3/src/scf2phd.c:376:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(data->strings->chunk + data->strings->used, key, l_key);
data/caftools-2.0.3/src/scf2phd.c:379:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(data->strings->chunk + data->strings->used, chem,    l_chem);
data/caftools-2.0.3/src/scf2phd.c:382:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(data->strings->chunk + data->strings->used, dye,     l_dye);
data/caftools-2.0.3/src/scf2phd.c:385:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(data->strings->chunk + data->strings->used, machine, l_machine);
data/caftools-2.0.3/src/scf2phd.c:452:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
static void get_chem_info(Read *read, char **chem, char **dye,
data/caftools-2.0.3/src/templates.c:98:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  CAFSEQ *read;            /* Current read CAFSEQ object */

ANALYSIS SUMMARY:

Hits = 745
Lines analyzed = 36579 in approximately 1.05 seconds (34759 lines/second)
Physical Source Lines of Code (SLOC) = 24950
Hits@level = [0] 674 [1] 309 [2] 288 [3]  12 [4] 136 [5]   0
Hits@level+ = [0+] 1419 [1+] 745 [2+] 436 [3+] 148 [4+] 136 [5+]   0
Hits/KSLOC@level+ = [0+] 56.8737 [1+] 29.8597 [2+] 17.4749 [3+] 5.93186 [4+] 5.4509 [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.