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/libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/Mosaik.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/Repeats.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/Repeats.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/SWMain.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp
Examining data/libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/convert.h
Examining data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp

FINAL RESULTS:

data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:110:13:  [3] (buffer) getopt_long:
  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.
        c = getopt_long (argc, argv, "hpRzm:n:g:r:e:b:r:",
data/libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:830:43:  [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).
                cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:840:35:  [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).
        cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:158:25:  [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).
            bandwidth = atoi(optarg);
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:241:23:  [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).
                len = atoi(slen.c_str());
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:246:23:  [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).
                len = atoi(slen.c_str());
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:252:23:  [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).
                len = atoi(slen.c_str());
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:258:23:  [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).
                len = atoi(slen.c_str());
data/libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:618:32:  [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).
	const unsigned int alLength = strlen(mReversedAnchor);
data/libsmithwaterman-0.0+git20160702.2610e25/SWMain.cpp:67:36:  [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).
	const unsigned int referenceLen = strlen(pReference);
data/libsmithwaterman-0.0+git20160702.2610e25/SWMain.cpp:68:36:  [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).
	const unsigned int queryLen     = strlen(pQuery);
data/libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:487:29:  [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).
    unsigned int alLength = strlen(mReversedAnchor);
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:15:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
string reverseComplement(string read) {
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:21:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	rc_read.assign(read.rbegin(), read.rend());
data/libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:21:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	rc_read.assign(read.rbegin(), read.rend());

ANALYSIS SUMMARY:

Hits = 15
Lines analyzed = 3213 in approximately 0.09 seconds (36541 lines/second)
Physical Source Lines of Code (SLOC) = 2115
Hits@level = [0]  13 [1]   7 [2]   7 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]  28 [1+]  15 [2+]   8 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 13.2388 [1+] 7.0922 [2+] 3.78251 [3+] 0.472813 [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.