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/iitii-0.0+git20191030.85209e0/src/iitii.h
Examining data/iitii-0.0+git20191030.85209e0/src/main.cpp
Examining data/iitii-0.0+git20191030.85209e0/test/gnomad_benchmark.cc
Examining data/iitii-0.0+git20191030.85209e0/test/util.h
Examining data/iitii-0.0+git20191030.85209e0/test/dumb_benchmark.cc
Examining data/iitii-0.0+git20191030.85209e0/test/test_iitii.cc
Examining data/iitii-0.0+git20191030.85209e0/debian/missing-sources/ctpl/ctpl_stl.h
Examining data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/hts_defs.h
Examining data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h
Examining data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/tbx.h

FINAL RESULTS:

data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/hts_defs.h:89:24:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define HTS_PRINTF_FMT printf
data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h:242:2:  [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(s->s + s->l, p, l);
data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h:275:2:  [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(s->s + s->l, p, l);
data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h:353:9:  [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(&cp[j-=2], d, 2);
data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h:380:2:  [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 buf[32];
data/iitii-0.0+git20191030.85209e0/src/iitii.h:338:16:  [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).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/iitii-0.0+git20191030.85209e0/src/iitii.h:356:20:  [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).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/iitii-0.0+git20191030.85209e0/src/iitii.h:421:18:  [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).
        int fd = open(filename.c_str(), O_RDWR);
data/iitii-0.0+git20191030.85209e0/test/util.h:165:18:  [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).
        vt.beg = atoi(tokens[1]);
data/iitii-0.0+git20191030.85209e0/debian/missing-sources/htslib/kstring.h:250:19:  [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).
	return kputsn(p, strlen(p), s);
data/iitii-0.0+git20191030.85209e0/test/util.h:36:39:  [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).
    return last_token ? (last_token + strlen(last_token) - s) : 0;
data/iitii-0.0+git20191030.85209e0/test/util.h:87:49:  [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).
            assert(ks_len((kstring_t*)&str_) == strlen(str_.s));

ANALYSIS SUMMARY:

Hits = 12
Lines analyzed = 2351 in approximately 0.09 seconds (25652 lines/second)
Physical Source Lines of Code (SLOC) = 1652
Hits@level = [0]   0 [1]   3 [2]   8 [3]   0 [4]   1 [5]   0
Hits@level+ = [0+]  12 [1+]  12 [2+]   9 [3+]   1 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 7.26392 [1+] 7.26392 [2+] 5.44794 [3+] 0.605327 [4+] 0.605327 [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.