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/transtermhp-2.09/ermolaeva-score.h
Examining data/transtermhp-2.09/2ndscore.cc
Examining data/transtermhp-2.09/ermolaeva-score.cc
Examining data/transtermhp-2.09/search.cc
Examining data/transtermhp-2.09/analysis.cc
Examining data/transtermhp-2.09/transterm.h
Examining data/transtermhp-2.09/transterm.cc
Examining data/transtermhp-2.09/util.cc
Examining data/transtermhp-2.09/conf.cc
Examining data/transtermhp-2.09/distr.h
Examining data/transtermhp-2.09/search.h
Examining data/transtermhp-2.09/anti.cc
Examining data/transtermhp-2.09/distr.cc
Examining data/transtermhp-2.09/gene-reader.cc
Examining data/transtermhp-2.09/map-output.h
Examining data/transtermhp-2.09/gene-reader.h
Examining data/transtermhp-2.09/util.h
Examining data/transtermhp-2.09/analysis.h
Examining data/transtermhp-2.09/map-output.cc
Examining data/transtermhp-2.09/conf.h
Examining data/transtermhp-2.09/seq.h
Examining data/transtermhp-2.09/ermolaeva-oldconf.cc
Examining data/transtermhp-2.09/seq.cc

FINAL RESULTS:

data/transtermhp-2.09/2ndscore.cc:94:14:  [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.
    while((a=getopt_long(argc, argv, OPTIONS, long_options, 0)) != -1)
data/transtermhp-2.09/transterm.cc:141:14:  [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.
    while((a=getopt_long(argc, argv, OPTIONS, long_options, 0)) != -1)
data/transtermhp-2.09/2ndscore.cc:109:42:  [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).
            case MINSTEM_OPT: MIN_STEM = atoi(optarg); break;
data/transtermhp-2.09/2ndscore.cc:110:42:  [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).
            case MINLOOP_OPT: MIN_LOOP = atoi(optarg); break;
data/transtermhp-2.09/2ndscore.cc:111:36:  [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).
            case MAXLEN_OPT: len = atoi(optarg); break;
data/transtermhp-2.09/2ndscore.cc:112:38:  [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).
            case MAXLOOP_OPT: loop = atoi(optarg); break;
data/transtermhp-2.09/gene-reader.cc:72:17:  [2] (integer) atol:
  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).
        start = atol(locvec[0].c_str());
data/transtermhp-2.09/gene-reader.cc:73:15:  [2] (integer) atol:
  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).
        end = atol(locvec[2].c_str());
data/transtermhp-2.09/seq.cc:170:5:  [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(newseq + padding, dna.dna, dna.length);
data/transtermhp-2.09/transterm.cc:156:42:  [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).
            case MINSTEM_OPT: MIN_STEM = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:157:42:  [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).
            case MINLOOP_OPT: MIN_LOOP = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:158:46:  [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).
            case UWINLEN_OPT: UWINDOW_SIZE = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:159:49:  [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).
            case UWINREQ_OPT: UWINDOW_REQUIRE = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:162:36:  [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).
            case MAXLEN_OPT: len = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:163:38:  [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).
            case MAXLOOP_OPT: loop = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:169:49:  [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).
            case STARTCUT_OPT: gene_start_cut = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:170:45:  [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).
            case ENDCUT_OPT: gene_end_cut = atoi(optarg); break;
data/transtermhp-2.09/transterm.cc:198:37:  [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).
            case 'c': conf_cutoff = atoi(optarg); break;

ANALYSIS SUMMARY:

Hits = 18
Lines analyzed = 5651 in approximately 0.12 seconds (47815 lines/second)
Physical Source Lines of Code (SLOC) = 4041
Hits@level = [0]   0 [1]   0 [2]  16 [3]   2 [4]   0 [5]   0
Hits@level+ = [0+]  18 [1+]  18 [2+]  18 [3+]   2 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 4.45434 [1+] 4.45434 [2+] 4.45434 [3+] 0.494927 [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.