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/libfastahack-1.0.0+dfsg/Fasta.cpp
Examining data/libfastahack-1.0.0+dfsg/Fasta.h
Examining data/libfastahack-1.0.0+dfsg/FastaHack.cpp
Examining data/libfastahack-1.0.0+dfsg/LargeFileSupport.h
Examining data/libfastahack-1.0.0+dfsg/Region.h
Examining data/libfastahack-1.0.0+dfsg/split.cpp
Examining data/libfastahack-1.0.0+dfsg/split.h

FINAL RESULTS:

data/libfastahack-1.0.0+dfsg/split.cpp:21:5:  [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(cstr, s.c_str());
data/libfastahack-1.0.0+dfsg/FastaHack.cpp:65:13:  [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, "hciedr:",
data/libfastahack-1.0.0+dfsg/Fasta.cpp:48:15:  [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).
    indexFile.open(fname.c_str(), ifstream::in);
data/libfastahack-1.0.0+dfsg/Fasta.cpp:60:73:  [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).
                this->insert(make_pair(name, FastaIndexEntry(fields[0], atoi(fields[1].c_str()),
data/libfastahack-1.0.0+dfsg/Fasta.cpp:62:53:  [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).
                                                    atoi(fields[3].c_str()),
data/libfastahack-1.0.0+dfsg/Fasta.cpp:63:53:  [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).
                                                    atoi(fields[4].c_str()))));
data/libfastahack-1.0.0+dfsg/Fasta.cpp:136:13:  [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).
    refFile.open(refname.c_str());
data/libfastahack-1.0.0+dfsg/Fasta.cpp:218:10:  [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).
    file.open(fname.c_str()); 
data/libfastahack-1.0.0+dfsg/Fasta.cpp:248:22:  [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).
void FastaReference::open(string reffilename) {
data/libfastahack-1.0.0+dfsg/Fasta.cpp:250:18:  [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 (!(file = fopen(filename.c_str(), "r"))) {
data/libfastahack-1.0.0+dfsg/Fasta.h:62:14:  [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).
        void open(string reffilename);
data/libfastahack-1.0.0+dfsg/FastaHack.cpp:140:8:  [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).
    fr.open(fastaFileName);
data/libfastahack-1.0.0+dfsg/Region.h:27:28:  [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).
                startPos = atoi(region.substr(foundFirstColon + 1).c_str());
data/libfastahack-1.0.0+dfsg/Region.h:31:18:  [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).
		    startPos = atoi(region.substr(foundFirstColon + 1, foundRangeDots - foundRangeDots - 1).c_str());
data/libfastahack-1.0.0+dfsg/Region.h:32:17:  [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).
		    stopPos = atoi(region.substr(foundRangeDots + 2).c_str()); // to the start of this chromosome
data/libfastahack-1.0.0+dfsg/Region.h:34:18:  [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).
		    startPos = atoi(region.substr(foundFirstColon + 1, foundRangeDash - foundRangeDash - 1).c_str());
data/libfastahack-1.0.0+dfsg/Region.h:35:17:  [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).
		    stopPos = atoi(region.substr(foundRangeDash + 1).c_str()); // to the start of this chromosome
data/libfastahack-1.0.0+dfsg/split.cpp:19:5:  [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 cchars [s.size()+1];

ANALYSIS SUMMARY:

Hits = 18
Lines analyzed = 735 in approximately 0.06 seconds (12992 lines/second)
Physical Source Lines of Code (SLOC) = 576
Hits@level = [0]   5 [1]   0 [2]  16 [3]   1 [4]   1 [5]   0
Hits@level+ = [0+]  23 [1+]  18 [2+]  18 [3+]   2 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 39.9306 [1+] 31.25 [2+] 31.25 [3+] 3.47222 [4+] 1.73611 [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.