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-bx-0.8.8/lib/bx/align/sitemask/find_cpg.c
Examining data/python-bx-0.8.8/lib/bx/align/sitemask/find_cpg.h
Examining data/python-bx-0.8.8/src/binBits.c
Examining data/python-bx-0.8.8/src/binBits.h
Examining data/python-bx-0.8.8/src/bunzip/micro-bunzip.c
Examining data/python-bx-0.8.8/src/bunzip/micro-bunzip.h
Examining data/python-bx-0.8.8/src/cluster.c
Examining data/python-bx-0.8.8/src/cluster.h
Examining data/python-bx-0.8.8/src/kent/bits.c
Examining data/python-bx-0.8.8/src/kent/bits.h
Examining data/python-bx-0.8.8/src/kent/common.c
Examining data/python-bx-0.8.8/src/kent/common.h
Examining data/python-bx-0.8.8/src/npy_capsule_as_void_ptr.h
Examining data/python-bx-0.8.8/src/pwm_utils.c
Examining data/python-bx-0.8.8/src/pwm_utils.h
Examining data/python-bx-0.8.8/src/samtools/bgzf.c
Examining data/python-bx-0.8.8/src/samtools/bgzf.h
Examining data/python-bx-0.8.8/src/samtools/khash.h

FINAL RESULTS:

data/python-bx-0.8.8/src/bunzip/micro-bunzip.c:85:11:  [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.
	unsigned char selectors[32768];			/* nSelectors=15 bits */
data/python-bx-0.8.8/src/bunzip/micro-bunzip.c:131:11:  [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.
	unsigned char uc, symToByte[256], mtfSymbol[256], *selectors;
data/python-bx-0.8.8/src/bunzip/micro-bunzip.c:187:12:  [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.
		unsigned char length[MAX_SYMBOLS],temp[MAX_HUFCODE_BITS+1];
data/python-bx-0.8.8/src/bunzip/micro-bunzip.h:59:11:  [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.
	unsigned char selectors[32768];			/* nSelectors=15 bits */
data/python-bx-0.8.8/src/kent/bits.c:64:9:  [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(bits, orig, byteCount);
data/python-bx-0.8.8/src/samtools/bgzf.c:198:8:  [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).
		fd = open(path, oflag);
data/python-bx-0.8.8/src/samtools/bgzf.c:207:8:  [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).
		fd = open(path, oflag, 0666);
data/python-bx-0.8.8/src/samtools/bgzf.c:330:9:  [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(fp->uncompressed_block,
data/python-bx-0.8.8/src/samtools/bgzf.c:406:2:  [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(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
data/python-bx-0.8.8/src/samtools/bgzf.c:439:2:  [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(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
data/python-bx-0.8.8/src/samtools/bgzf.c:472:5:  [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(compressed_block, header, BLOCK_HEADER_LENGTH);
data/python-bx-0.8.8/src/samtools/bgzf.c:524:9:  [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(output, buffer + fp->block_offset, copy_length);
data/python-bx-0.8.8/src/samtools/bgzf.c:582:9:  [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(buffer + fp->block_offset, input, copy_length);
data/python-bx-0.8.8/src/bunzip/micro-bunzip.c:102:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			if((bd->inbufCount = read(bd->in_fd, bd->inbuf, IOBUF_SIZE)) <= 0)
data/python-bx-0.8.8/src/bunzip/micro-bunzip.c:701:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    else if(read(0,&c,1)) fprintf(stderr,"Trailing garbage ignored\n");
data/python-bx-0.8.8/src/pwm_utils.c:11:27:  [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).
        int string_size = strlen(argv[1]);
data/python-bx-0.8.8/src/pwm_utils.c:12:13:  [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).
        if (strlen(argv[2]) != string_size) {

ANALYSIS SUMMARY:

Hits = 17
Lines analyzed = 3377 in approximately 0.14 seconds (23623 lines/second)
Physical Source Lines of Code (SLOC) = 2327
Hits@level = [0]  11 [1]   4 [2]  13 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  28 [1+]  17 [2+]  13 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 12.0327 [1+] 7.30554 [2+] 5.58659 [3+]   0 [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.