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/ncbi-seg-0.0.20000620/lnfac.h
Examining data/ncbi-seg-0.0.20000620/hiseg.c
Examining data/ncbi-seg-0.0.20000620/genwin.h
Examining data/ncbi-seg-0.0.20000620/debian/patches/genwin.c
Examining data/ncbi-seg-0.0.20000620/debian/patches/seg.c
Examining data/ncbi-seg-0.0.20000620/seg.c
Examining data/ncbi-seg-0.0.20000620/genwin.c

FINAL RESULTS:

data/ncbi-seg-0.0.20000620/genwin.c:97:7:  [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(dbase->filename, blastdir);
data/ncbi-seg-0.0.20000620/genwin.c:98:7:  [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(dbase->filename, name);
data/ncbi-seg-0.0.20000620/genwin.c:99:7:  [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(dbase->indexname, indexdir);
data/ncbi-seg-0.0.20000620/genwin.c:100:7:  [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(dbase->indexname, name);
data/ncbi-seg-0.0.20000620/genwin.c:106:7:  [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(dbase->filename, name);
data/ncbi-seg-0.0.20000620/genwin.c:107:7:  [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(dbase->indexname, name);
data/ncbi-seg-0.0.20000620/hiseg.c:709:2:  [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(stdout, format, 1);
data/ncbi-seg-0.0.20000620/hiseg.c:715:4:  [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(stdout, format, i+1);
data/ncbi-seg-0.0.20000620/seg.c:697:2:  [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(stdout, format, 1);
data/ncbi-seg-0.0.20000620/seg.c:703:4:  [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(stdout, format, i+1);
data/ncbi-seg-0.0.20000620/hiseg.c:135:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
   while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1)
data/ncbi-seg-0.0.20000620/seg.c:137:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
   while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1)
data/ncbi-seg-0.0.20000620/genwin.c:44:10:  [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.
unsigned char	aaflag[128];
data/ncbi-seg-0.0.20000620/genwin.c:45:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char aachar[20];
data/ncbi-seg-0.0.20000620/genwin.c:49:4:  [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 string[STRSIZE];
data/ncbi-seg-0.0.20000620/genwin.c:114:24:  [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 ((dbase->fp=fopen(dbase->filename, "r"))==NULL)
data/ncbi-seg-0.0.20000620/genwin.c:240:4:  [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(win->seq, (parent->seq)+start, length);
data/ncbi-seg-0.0.20000620/genwin.c:622:4:  [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(seq->id, bptr, idend);
data/ncbi-seg-0.0.20000620/genwin.c:640:4:  [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(seq->name, bptr, namend);
data/ncbi-seg-0.0.20000620/genwin.c:659:4:  [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(seq->organism, bptr, orgend);
data/ncbi-seg-0.0.20000620/hiseg.c:110:19:  [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).
         window = atoi(argv[2]);
data/ncbi-seg-0.0.20000620/hiseg.c:140:24:  [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).
            hilenmin = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:187:24:  [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).
            charline = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:193:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            maxtrim = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:681:2:  [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	format[10];
data/ncbi-seg-0.0.20000620/hiseg.c:687:2:  [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(format, "%%%dd ", leftspace);
data/ncbi-seg-0.0.20000620/hiseg.c:737:2:  [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	buffer[100], leftfmt[20], rightfmt[20];
data/ncbi-seg-0.0.20000620/hiseg.c:746:2:  [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(leftfmt, "%%%ds", cline);
data/ncbi-seg-0.0.20000620/hiseg.c:747:2:  [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(rightfmt, "%%-%ds", cline);
data/ncbi-seg-0.0.20000620/hiseg.c:853:4:  [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 outbuf[HDRLEN+1];
data/ncbi-seg-0.0.20000620/seg.c:111:19:  [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).
         window = atoi(argv[2]);
data/ncbi-seg-0.0.20000620/seg.c:142:24:  [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).
            hilenmin = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:189:24:  [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).
            charline = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:195:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            maxtrim = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:669:2:  [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	format[10];
data/ncbi-seg-0.0.20000620/seg.c:675:2:  [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(format, "%%%dd ", leftspace);
data/ncbi-seg-0.0.20000620/seg.c:725:2:  [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	buffer[100], leftfmt[20], rightfmt[20];
data/ncbi-seg-0.0.20000620/seg.c:734:2:  [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(leftfmt, "%%%ds", cline);
data/ncbi-seg-0.0.20000620/seg.c:735:2:  [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(rightfmt, "%%-%ds", cline);
data/ncbi-seg-0.0.20000620/seg.c:841:4:  [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 outbuf[HDRLEN+1];
data/ncbi-seg-0.0.20000620/genwin.c:95:41:  [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).
      dbase->filename = (char *) malloc(strlen(blastdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:95:58:  [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).
      dbase->filename = (char *) malloc(strlen(blastdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:96:42:  [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).
      dbase->indexname = (char *) malloc(strlen(indexdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:96:59:  [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).
      dbase->indexname = (char *) malloc(strlen(indexdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:104:41:  [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).
      dbase->filename = (char *) malloc(strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:105:42:  [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).
      dbase->indexname = (char *) malloc(strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:516:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = getc(dbase->fp);
data/ncbi-seg-0.0.20000620/genwin.c:523:17:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      while ((c=getc(dbase->fp)) != EOF && c !='\n')
data/ncbi-seg-0.0.20000620/genwin.c:555:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   if ((c=getc(fp)) == EOF)
data/ncbi-seg-0.0.20000620/genwin.c:563:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = getc(fp);
data/ncbi-seg-0.0.20000620/genwin.c:575:24:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   for (i=0,itotal=0,c=getc(fp); c != EOF; c=getc(fp))
data/ncbi-seg-0.0.20000620/genwin.c:575:46:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   for (i=0,itotal=0,c=getc(fp); c != EOF; c=getc(fp))
data/ncbi-seg-0.0.20000620/genwin.c:665:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = getc(fp);
data/ncbi-seg-0.0.20000620/genwin.c:689:14:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   while ((c=getc(fp))!='\n' && c!=EOF)
data/ncbi-seg-0.0.20000620/genwin.c:734:30:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	for (i = 0, itotal = 0, c = getc(fp); c != EOF; c = getc(fp)) {
data/ncbi-seg-0.0.20000620/genwin.c:734:54:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	for (i = 0, itotal = 0, c = getc(fp); c != EOF; c = getc(fp)) {
data/ncbi-seg-0.0.20000620/genwin.c:788:16:  [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->length = strlen(seq->seq);
data/ncbi-seg-0.0.20000620/hiseg.c:884:20:  [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).
		 i = MIN(HDRLEN, strlen(header));
data/ncbi-seg-0.0.20000620/seg.c:872:20:  [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).
		 i = MIN(HDRLEN, strlen(header));

ANALYSIS SUMMARY:

Hits = 59
Lines analyzed = 4322 in approximately 0.23 seconds (18488 lines/second)
Physical Source Lines of Code (SLOC) = 3489
Hits@level = [0]  41 [1]  19 [2]  28 [3]   2 [4]  10 [5]   0
Hits@level+ = [0+] 100 [1+]  59 [2+]  40 [3+]  12 [4+]  10 [5+]   0
Hits/KSLOC@level+ = [0+] 28.6615 [1+] 16.9103 [2+] 11.4646 [3+] 3.43938 [4+] 2.86615 [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.