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/clonalframeml-1.12/src/bank/MLST.h
Examining data/clonalframeml-1.12/src/bank/approxdf.h
Examining data/clonalframeml-1.12/src/bank/census.h
Examining data/clonalframeml-1.12/src/bank/cmatrix.h
Examining data/clonalframeml-1.12/src/bank/coalesce.h
Examining data/clonalframeml-1.12/src/bank/coalescent_control.h
Examining data/clonalframeml-1.12/src/bank/coalescent_process.h
Examining data/clonalframeml-1.12/src/bank/controlwizard.h
Examining data/clonalframeml-1.12/src/bank/ess.h
Examining data/clonalframeml-1.12/src/bank/mutation.h
Examining data/clonalframeml-1.12/src/bank/pause.h
Examining data/clonalframeml-1.12/src/bank/revolver.h
Examining data/clonalframeml-1.12/src/bank/sort.h
Examining data/clonalframeml-1.12/src/bank/tsv.h
Examining data/clonalframeml-1.12/src/brent.h
Examining data/clonalframeml-1.12/src/coalesce/coalescent_record.h
Examining data/clonalframeml-1.12/src/main.cpp
Examining data/clonalframeml-1.12/src/main.h
Examining data/clonalframeml-1.12/src/myutils/DNA.h
Examining data/clonalframeml-1.12/src/myutils/argumentwizard.h
Examining data/clonalframeml-1.12/src/myutils/lotri_matrix.h
Examining data/clonalframeml-1.12/src/myutils/matrix.h
Examining data/clonalframeml-1.12/src/myutils/mydouble.h
Examining data/clonalframeml-1.12/src/myutils/myerror.h
Examining data/clonalframeml-1.12/src/myutils/myutils.h
Examining data/clonalframeml-1.12/src/myutils/newick.h
Examining data/clonalframeml-1.12/src/myutils/random.h
Examining data/clonalframeml-1.12/src/myutils/utils.h
Examining data/clonalframeml-1.12/src/myutils/vector.h
Examining data/clonalframeml-1.12/src/powell.h
Examining data/clonalframeml-1.12/src/xmfa.h

FINAL RESULTS:

data/clonalframeml-1.12/src/bank/coalescent_process.h:568:14:  [2] (misc) fopen:
  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).
		FILE* fout=fopen(filename,"w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:610:14:  [2] (misc) fopen:
  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).
		FILE* fout=fopen(filename,"w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:648:14:  [2] (misc) fopen:
  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).
		FILE* fout=fopen(filename,"w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:681:18:  [2] (misc) fopen:
  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).
		FILE *ageout = fopen(ageout_file.str().c_str(), "w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:682:19:  [2] (misc) fopen:
  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).
		FILE *treeout = fopen(treeout_file.str().c_str(), "w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:712:19:  [2] (misc) fopen:
  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).
		FILE *tpicout = fopen("tpic.bat","w");
data/clonalframeml-1.12/src/bank/coalescent_process.h:717:23:  [2] (misc) fopen:
  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).
		FILE *viewtpicout = fopen("viewtpic.bat","w");
data/clonalframeml-1.12/src/bank/controlwizard.h:452:13:  [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).
		int value=atoi(word.c_str());
data/clonalframeml-1.12/src/bank/controlwizard.h:615:19:  [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).
			ptr->push_back(atoi(words[i].c_str()));
data/clonalframeml-1.12/src/main.cpp:1210:15:  [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.
	static const char AGCTN[5] = {'A','G','C','T','N'};
data/clonalframeml-1.12/src/main.cpp:1736:15:  [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.
	static const char AGCTN[5] = {'A','G','C','T','N'};
data/clonalframeml-1.12/src/bank/tsv.h:46:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	tsv& read(const char* infilename)
data/clonalframeml-1.12/src/main.cpp:1848:6:  [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(chr_name)==0) 
data/clonalframeml-1.12/src/main.cpp:1859:10:  [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(chr_name)==0) 
data/clonalframeml-1.12/src/main.cpp:1872:8:  [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(chr_name)==0)

ANALYSIS SUMMARY:

Hits = 15
Lines analyzed = 13196 in approximately 0.48 seconds (27606 lines/second)
Physical Source Lines of Code (SLOC) = 10385
Hits@level = [0]  75 [1]   4 [2]  11 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  90 [1+]  15 [2+]  11 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 8.66635 [1+] 1.44439 [2+] 1.05922 [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.