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/sibelia-3.0.7+dfsg/src/platform.cpp
Examining data/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp
Examining data/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp
Examining data/sibelia-3.0.7+dfsg/src/postprocessor.h
Examining data/sibelia-3.0.7+dfsg/src/blockinstance.cpp
Examining data/sibelia-3.0.7+dfsg/src/dnasequence.h
Examining data/sibelia-3.0.7+dfsg/src/sibelia.cpp
Examining data/sibelia-3.0.7+dfsg/src/hashing.h
Examining data/sibelia-3.0.7+dfsg/src/util.h
Examining data/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp
Examining data/sibelia-3.0.7+dfsg/src/unrolledlist.h
Examining data/sibelia-3.0.7+dfsg/src/indexedsequence.cpp
Examining data/sibelia-3.0.7+dfsg/src/stranditerator.cpp
Examining data/sibelia-3.0.7+dfsg/src/synteny.cpp
Examining data/sibelia-3.0.7+dfsg/src/outputgenerator.h
Examining data/sibelia-3.0.7+dfsg/src/blockfinder.cpp
Examining data/sibelia-3.0.7+dfsg/src/fasta.cpp
Examining data/sibelia-3.0.7+dfsg/src/fasta.h
Examining data/sibelia-3.0.7+dfsg/src/platform.h
Examining data/sibelia-3.0.7+dfsg/src/resource.h
Examining data/sibelia-3.0.7+dfsg/src/blockfinder.h
Examining data/sibelia-3.0.7+dfsg/src/bifurcationstorage.h
Examining data/sibelia-3.0.7+dfsg/src/indexedsequence.h
Examining data/sibelia-3.0.7+dfsg/src/postprocessor.cpp
Examining data/sibelia-3.0.7+dfsg/src/blockinstance.h
Examining data/sibelia-3.0.7+dfsg/src/edge.cpp
Examining data/sibelia-3.0.7+dfsg/src/serialization.cpp
Examining data/sibelia-3.0.7+dfsg/src/dnasequence.cpp
Examining data/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp
Examining data/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h
Examining data/sibelia-3.0.7+dfsg/src/util.cpp
Examining data/sibelia-3.0.7+dfsg/src/resource.cpp
Examining data/sibelia-3.0.7+dfsg/src/common.h
Examining data/sibelia-3.0.7+dfsg/src/outputgenerator.cpp

FINAL RESULTS:

data/sibelia-3.0.7+dfsg/src/serialization.cpp:22:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(&buf[0], "[color=\"%s\", label=\"(%i, %i)\"];", color.c_str(), static_cast<int>(chr), static_cast<int>(pos));
data/sibelia-3.0.7+dfsg/src/serialization.cpp:105:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(&buf[0], "[color=\"%s\", label=\"chr=%i pos=%i len=%i orpos=%i orlen=%i  ch='%c'\"];", color.c_str(), uchr, upos, ulength, uorpos, uorlength, edge[i].GetFirstChar());
data/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:176:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    	list.push_back(random);
data/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:177:25:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    	testList.push_back(random);
data/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:184:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand((unsigned)time(0));
data/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:564:10:  [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).
		stream.open(fileName.c_str());
data/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:576:11:  [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).
			stream.open((*itDirs + "/" + fileName).c_str());
data/sibelia-3.0.7+dfsg/src/platform.cpp:70:31:  [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).
			if(notExists && (handle_ = fopen(path_.c_str(), "w+b")) != 0)
data/sibelia-3.0.7+dfsg/src/serialization.cpp:20:4:  [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.
			char buf[1 << 8];
data/sibelia-3.0.7+dfsg/src/serialization.cpp:97:4:  [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.
			char buf[1 << 8];
data/sibelia-3.0.7+dfsg/src/hashing.h:122:16:  [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.
			return std::mismatch(it1, end1, it2).first == end1;

ANALYSIS SUMMARY:

Hits = 11
Lines analyzed = 13752 in approximately 0.54 seconds (25357 lines/second)
Physical Source Lines of Code (SLOC) = 12662
Hits@level = [0]   1 [1]   1 [2]   5 [3]   3 [4]   2 [5]   0
Hits@level+ = [0+]  12 [1+]  11 [2+]  10 [3+]   5 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 0.947718 [1+] 0.868741 [2+] 0.789765 [3+] 0.394882 [4+] 0.157953 [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.