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/transrate-tools-1.0.0/src/bam-read.cpp Examining data/transrate-tools-1.0.0/src/pileup.cpp Examining data/transrate-tools-1.0.0/src/segmenter.cpp Examining data/transrate-tools-1.0.0/src/segmenter.h Examining data/transrate-tools-1.0.0/src/bam-read.h Examining data/transrate-tools-1.0.0/src/pileup.h FINAL RESULTS: data/transrate-tools-1.0.0/src/bam-read.cpp:92:13: [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). len = atoi(it[i].Length.c_str()); data/transrate-tools-1.0.0/src/bam-read.cpp:197:12: [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). output.open (argv[2]); ANALYSIS SUMMARY: Hits = 2 Lines analyzed = 591 in approximately 0.02 seconds (27301 lines/second) Physical Source Lines of Code (SLOC) = 449 Hits@level = [0] 0 [1] 0 [2] 2 [3] 0 [4] 0 [5] 0 Hits@level+ = [0+] 2 [1+] 2 [2+] 2 [3+] 0 [4+] 0 [5+] 0 Hits/KSLOC@level+ = [0+] 4.45434 [1+] 4.45434 [2+] 4.45434 [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.