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/flexbar-3.5.0/src/Flexbar.cpp
Examining data/flexbar-3.5.0/src/Flexbar.h
Examining data/flexbar-3.5.0/src/FlexbarIO.h
Examining data/flexbar-3.5.0/src/FlexbarTypes.h
Examining data/flexbar-3.5.0/src/LoadAdapters.h
Examining data/flexbar-3.5.0/src/LoadFasta.h
Examining data/flexbar-3.5.0/src/Options.h
Examining data/flexbar-3.5.0/src/PairedAlign.h
Examining data/flexbar-3.5.0/src/PairedInput.h
Examining data/flexbar-3.5.0/src/PairedOutput.h
Examining data/flexbar-3.5.0/src/QualTrimming.h
Examining data/flexbar-3.5.0/src/SeqAlign.h
Examining data/flexbar-3.5.0/src/SeqAlignAlgo.h
Examining data/flexbar-3.5.0/src/SeqAlignPair.h
Examining data/flexbar-3.5.0/src/SeqInput.h
Examining data/flexbar-3.5.0/src/SeqOutput.h
Examining data/flexbar-3.5.0/src/SeqOutputFiles.h

FINAL RESULTS:

data/flexbar-3.5.0/src/FlexbarIO.h:26:7:  [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).
	strm.open(path.c_str(), ios::in | ios::binary);
data/flexbar-3.5.0/src/FlexbarIO.h:37:7:  [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).
	strm.open(path.c_str(), ios::out | ios::binary);
data/flexbar-3.5.0/src/FlexbarIO.h:80:13:  [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 char const * VALUE[1];
data/flexbar-3.5.0/src/FlexbarIO.h:123:13:  [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 char const * VALUE[1];
data/flexbar-3.5.0/src/FlexbarIO.h:172:13:  [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 char const * VALUE[1];
data/flexbar-3.5.0/src/FlexbarIO.h:290:8:  [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).
		if(! open(seqFileIn, path.c_str())){
data/flexbar-3.5.0/src/LoadFasta.h:38:8:  [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).
		if(! open(seqFileIn, filePath.c_str())){
data/flexbar-3.5.0/src/SeqInput.h:45:9:  [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).
			if(! open(seqFileIn, cin)){
data/flexbar-3.5.0/src/SeqInput.h:51:9:  [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).
			if(! open(seqFileIn, filePath.c_str())){
data/flexbar-3.5.0/src/SeqOutput.h:59:9:  [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).
			if(! open(seqFileOut, cout)){
data/flexbar-3.5.0/src/SeqOutput.h:65:9:  [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).
			if(! open(seqFileOut, m_filePath.c_str())){
data/flexbar-3.5.0/src/SeqOutput.h:91:11:  [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).
		lstream.open(fname.c_str(), ios::out | ios::binary);
data/flexbar-3.5.0/src/SeqAlign.h:32:159:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	SeqAlign(tbb::concurrent_vector<flexbar::TBar> *queries, const Options &o, int minOverlap, float errorRate, const int tailLength, const int match, const int mismatch, const int gapCost, const bool isBarcoding):
data/flexbar-3.5.0/src/SeqAlign.h:50:32:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			m_algo(TAlgorithm(o, match, mismatch, gapCost, ! isBarcoding)){
data/flexbar-3.5.0/src/SeqAlignAlgo.h:29:60:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	SeqAlignAlgo(const Options &o, const int match, const int mismatch, const int gapCost, const bool isAdapterRm):
data/flexbar-3.5.0/src/SeqAlignAlgo.h:44:54:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				else setScore(m_scoreMatrix, TChar(i), TChar(j), mismatch);
data/flexbar-3.5.0/src/SeqAlignPair.h:31:105:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	SeqAlignPair(const Options &o, const int minOverlap, const float errorRate, const int match, const int mismatch, const int gapCost):
data/flexbar-3.5.0/src/SeqAlignPair.h:46:32:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			m_algo(TAlgorithm(o, match, mismatch, gapCost, true)){

ANALYSIS SUMMARY:

Hits = 18
Lines analyzed = 5146 in approximately 0.38 seconds (13599 lines/second)
Physical Source Lines of Code (SLOC) = 3507
Hits@level = [0]   0 [1]   6 [2]  12 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  18 [1+]  18 [2+]  12 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 5.13259 [1+] 5.13259 [2+] 3.42173 [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.