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/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c

FINAL RESULTS:

data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:90:15:  [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 (argc, argv, "M:N:G:b")) != -1) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.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 querySeq [MAX_SEQ_LENGTH];
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.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 queryAcc [MAX_ACC_LENGTH];
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.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 alignedTemplateSeq [2 * MAX_SEQ_LENGTH];
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.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 alignedQuerySeq [2 * MAX_SEQ_LENGTH];
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:93:12:  [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).
	  MATCH = atoi(optarg);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:96:15:  [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).
	  MISMATCH = atoi(optarg);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:99:10:  [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).
	  GAP = atoi(optarg);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:175:3:  [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 currSeq [MAX_SEQ_LENGTH];
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:179:14:  [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")) == NULL) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:215:14:  [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")) == NULL) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:184:21:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (letter = getc(fp)) != EOF) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:192:22:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	  while ( (letter = getc(fp)) != '\n') { ; }
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:221:18:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if ( (letter = getc(fp)) != '>') {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:225:22:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( ((letter = getc(fp)) != EOF) && (letter != ' ' && letter != '\n')) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:233:11:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	letter = getc(fp);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:236:21:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ( (letter = getc(fp)) != EOF) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:249:24:  [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).
  int querySeqLength = strlen(querySeq);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:476:33:  [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).
  int templateAlignmentLength = strlen(templateAlignment);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:477:30:  [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 queryAlignmentLength = strlen(queryAlignment);
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:500:19:  [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).
  for (i = 0, j = strlen(str) - 1; i < j; i++, j--) {
data/microbiomeutil-20101212+dfsg1/NAST-iEr/NAST-iEr.c:515:19:  [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).
  for (i = 0; i < strlen(sequence); i++) {

ANALYSIS SUMMARY:

Hits = 22
Lines analyzed = 628 in approximately 0.10 seconds (6096 lines/second)
Physical Source Lines of Code (SLOC) = 419
Hits@level = [0]  36 [1]  11 [2]  10 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]  58 [1+]  22 [2+]  11 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 138.425 [1+] 52.506 [2+] 26.253 [3+] 2.38663 [4+]   0 [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.