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/python-pybedtools-0.8.0/pybedtools/include/bedFile.cpp
Examining data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h
Examining data/python-pybedtools-0.8.0/pybedtools/include/fileType.cpp
Examining data/python-pybedtools-0.8.0/pybedtools/include/fileType.h
Examining data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp
Examining data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h
Examining data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h

FINAL RESULTS:

data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h:28:5:  [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, str.c_str());
data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h:42:5:  [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, str.c_str());
data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h:422:27:  [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).
            bed.start   = atoi(lineVector[1].c_str());
data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h:423:27:  [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).
            bed.end     = atoi(lineVector[2].c_str());
data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h:486:27:  [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).
            bed.start   = atoi(lineVector[1].c_str()) - 1;  // VCF is one-based
data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h:536:31:  [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).
                bed.start   = atoi(lineVector[3].c_str()) - 1;
data/python-pybedtools-0.8.0/pybedtools/include/bedFile.h:537:31:  [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).
                bed.end     = atoi(lineVector[4].c_str());
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:45:27:  [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).
gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:53:5:  [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  fmode[10];
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:88:5:  [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( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:142:5:  [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).
    open( name, mode);
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:149:20:  [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 gzstreambase::open( const char* name, int open_mode) {
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.cpp:150:16:  [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).
    if ( ! buf.open( name, open_mode))
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:51:5:  [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             buffer[bufferSize]; // data buffer
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:65:18:  [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).
    gzstreambuf* open( const char* name, int open_mode);
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:81:10:  [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).
    void open( const char* name, int open_mode);
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:98:10:  [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).
    void open( const char* name, int open_mode = std::ios::in) {
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:99:23:  [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).
        gzstreambase::open( name, open_mode);
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:109:10:  [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).
    void open( const char* name, int open_mode = std::ios::out) {
data/python-pybedtools-0.8.0/pybedtools/include/gzstream.h:110:23:  [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).
        gzstreambase::open( name, open_mode);
data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h:26:5:  [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 [str.size()+1];
data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h:40:5:  [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 [str.size()+1];
data/python-pybedtools-0.8.0/pybedtools/include/lineFileUtilities.h:45:25:  [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).
        elems.push_back(atoi(tok));
data/python-pybedtools-0.8.0/pybedtools/include/fileType.cpp:53:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
       if (!f.read((char*)&gzip_header, sizeof(gzip_header)))

ANALYSIS SUMMARY:

Hits = 24
Lines analyzed = 1422 in approximately 0.12 seconds (12339 lines/second)
Physical Source Lines of Code (SLOC) = 899
Hits@level = [0]   1 [1]   1 [2]  21 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+]  25 [1+]  24 [2+]  23 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 27.8087 [1+] 26.6963 [2+] 25.584 [3+] 2.22469 [4+] 2.22469 [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.