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/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Arg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ArgException.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ArgTraits.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLine.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLineInterface.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLineOutput.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Constraint.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/DocBookOutput.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/HelpVisitor.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/MultiArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/MultiSwitchArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/StandardTraits.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/StdOutput.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/SwitchArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/UnlabeledValueArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ValueArg.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ValuesConstraint.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/VersionVisitor.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Visitor.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/XorHandler.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ZshCompletionOutput.h
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test7.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test13.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test12.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test17-a.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test10.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test4.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test20.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test2.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test3.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test19.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test8.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test16.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test6.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test18.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test1.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test14.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test21.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test17.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test11.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test15.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test5.cpp
Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test9.cpp
Examining data/m2m-aligner-1.2/mmEM.h
Examining data/m2m-aligner-1.2/util.h
Examining data/m2m-aligner-1.2/mmEM.cpp
Examining data/m2m-aligner-1.2/param.h
Examining data/m2m-aligner-1.2/mmAligner.cpp

FINAL RESULTS:

data/m2m-aligner-1.2/mmEM.cpp:39:12:  [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).
		INITFILE.open(myParam.initFile.c_str());
data/m2m-aligner-1.2/mmEM.cpp:162:12:  [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).
		INITFILE.open(myParam.initFile.c_str());
data/m2m-aligner-1.2/mmEM.cpp:557:12:  [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).
	INPUTFILE.open(filename.c_str());
data/m2m-aligner-1.2/mmEM.cpp:665:13:  [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).
	ALIGNEROUT.open(myParam.alignerOut.c_str());
data/m2m-aligner-1.2/mmEM.cpp:693:12:  [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).
	ALIGNERIN.open(myParam.alignerIn.c_str());
data/m2m-aligner-1.2/mmEM.cpp:1074:10:  [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).
	ALIGNED.open(myParam.outputFilename.c_str());
data/m2m-aligner-1.2/mmEM.cpp:1075:12:  [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).
	NOALIGNED.open(string(myParam.outputFilename + ".err").c_str());

ANALYSIS SUMMARY:

Hits = 7
Lines analyzed = 8696 in approximately 0.38 seconds (22909 lines/second)
Physical Source Lines of Code (SLOC) = 4709
Hits@level = [0]   0 [1]   0 [2]   7 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   7 [1+]   7 [2+]   7 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 1.48652 [1+] 1.48652 [2+] 1.48652 [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.