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/tiddit-2.12.0+dfsg/src/TIDDIT.cpp
Examining data/tiddit-2.12.0+dfsg/src/common.h
Examining data/tiddit-2.12.0+dfsg/src/data_structures/CoverageModule.cpp
Examining data/tiddit-2.12.0+dfsg/src/data_structures/ProgramModules.h
Examining data/tiddit-2.12.0+dfsg/src/data_structures/Translocation.cpp
Examining data/tiddit-2.12.0+dfsg/src/data_structures/Translocation.h
Examining data/tiddit-2.12.0+dfsg/src/data_structures/findTranslocationsOnTheFly.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/Data_Exception.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/Data_Exception.h
Examining data/tiddit-2.12.0+dfsg/src/errors/Data_Not_Found.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/Data_Not_Found.h
Examining data/tiddit-2.12.0+dfsg/src/errors/File_Not_Found.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/File_Not_Found.h
Examining data/tiddit-2.12.0+dfsg/src/errors/Generic_Exception.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/Generic_Exception.h
Examining data/tiddit-2.12.0+dfsg/src/errors/Incorrect_Format.cpp
Examining data/tiddit-2.12.0+dfsg/src/errors/Incorrect_Format.h

FINAL RESULTS:

data/tiddit-2.12.0+dfsg/src/TIDDIT.cpp:292:13:  [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).
			gcOutput.open((outputfile+".gc.wig").c_str());
data/tiddit-2.12.0+dfsg/src/data_structures/CoverageModule.cpp:31:18:  [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).
		coverageOutput.open((output+".tab").c_str());
data/tiddit-2.12.0+dfsg/src/data_structures/CoverageModule.cpp:33:18:  [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).
		coverageOutput.open((output+".wig").c_str());
data/tiddit-2.12.0+dfsg/src/data_structures/Translocation.cpp:36:18:  [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).
	this->TIDDITVCF.open(intra_chr_eventsVCF.c_str());
data/tiddit-2.12.0+dfsg/src/data_structures/Translocation.cpp:90:20:  [2] (integer) atol:
  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).
			long splitPos = atol(SA_elements[1].c_str());

ANALYSIS SUMMARY:

Hits = 5
Lines analyzed = 1767 in approximately 0.06 seconds (28998 lines/second)
Physical Source Lines of Code (SLOC) = 1353
Hits@level = [0]   2 [1]   0 [2]   5 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   7 [1+]   5 [2+]   5 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 5.17369 [1+] 3.69549 [2+] 3.69549 [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.