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.