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/ragout-2.3/ragout/maf2synteny/cpp_impl/breakpoint_graph.cpp
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/breakpoint_graph.h
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/compress_algorithms.cpp
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/compress_algorithms.h
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/disjoint_set.h
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/maf_tools.cpp
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/maf_tools.h
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/main.cpp
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/permutation.cpp
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/permutation.h
Examining data/ragout-2.3/ragout/maf2synteny/cpp_impl/utility.h
Examining data/ragout-2.3/ragout/overlap/cpp_impl/build_graph.cpp
Examining data/ragout-2.3/ragout/overlap/cpp_impl/build_graph.h
Examining data/ragout-2.3/ragout/overlap/cpp_impl/fasta.cpp
Examining data/ragout-2.3/ragout/overlap/cpp_impl/fasta.h
Examining data/ragout-2.3/ragout/overlap/cpp_impl/main.cpp
Examining data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp
Examining data/ragout-2.3/ragout/overlap/cpp_impl/overlap.h
Examining data/ragout-2.3/ragout/overlap/cpp_impl/suffix_array.cpp
Examining data/ragout-2.3/ragout/overlap/cpp_impl/suffix_array.h

FINAL RESULTS:

data/ragout-2.3/ragout/maf2synteny/cpp_impl/main.cpp:208:16:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
	while ((opt = getopt(argc, argv, optString)) != -1)
data/ragout-2.3/ragout/maf2synteny/cpp_impl/maf_tools.cpp:143:15:  [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 start = atoi(tokens[3].c_str());
data/ragout-2.3/ragout/maf2synteny/cpp_impl/maf_tools.cpp:144:13:  [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 end = atoi(tokens[4].c_str());
data/ragout-2.3/ragout/maf2synteny/cpp_impl/maf_tools.cpp:151:45:  [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).
			if (attr.substr(0, 2) == "id") blockId = atoi(attr.substr(3).c_str());
data/ragout-2.3/ragout/maf2synteny/cpp_impl/main.cpp:96:11:  [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 k = atoi(buffer.substr(0, sep).c_str());
data/ragout-2.3/ragout/maf2synteny/cpp_impl/main.cpp:97:11:  [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 d = atoi(buffer.substr(sep + 1).c_str());
data/ragout-2.3/ragout/maf2synteny/cpp_impl/utility.h:29:2:  [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 cstr[128];
data/ragout-2.3/ragout/overlap/cpp_impl/main.cpp:52:51:  [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).
	return !makeOverlapGraph(posArgs[1], posArgs[2], atoi(posArgs[3].c_str()),
data/ragout-2.3/ragout/overlap/cpp_impl/main.cpp:53:9:  [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).
							 atoi(posArgs[4].c_str()), detectKmer, drawHist);
data/ragout-2.3/ragout/overlap/cpp_impl/suffix_array.cpp:44:92:  [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.
#define chr(_a) (cs == sizeof(sais_index_type) ? ((sais_index_type *)T)[(_a)] : ((unsigned char *)T)[(_a)])
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:117:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		if (read[read.length() - 1] == 'N') return;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:117:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		if (read[read.length() - 1] == 'N') return;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:118:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		long long l = c_[read[read.length() - 1]];
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		long long l = c_[read[read.length() - 1]];
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:119:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		long long r = c_[read[read.length() - 1] + 1] - 1;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:119:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		long long r = c_[read[read.length() - 1] + 1] - 1;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:120:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		int i = read.length() - 2;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:124:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			if (read[i] == 'N') return;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:125:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			l = c_[read[i]] + occ_[read[i]][l - 1];
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:125:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			l = c_[read[i]] + occ_[read[i]][l - 1];
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:126:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			r = c_[read[i]] + occ_[read[i]][r] - 1;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:126:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			r = c_[read[i]] + occ_[read[i]][r] - 1;
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:128:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			if ((int)read.length() - i >= minOverlap)
data/ragout-2.3/ragout/overlap/cpp_impl/overlap.cpp:140:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
														  read.length() - i));

ANALYSIS SUMMARY:

Hits = 24
Lines analyzed = 2925 in approximately 0.14 seconds (21485 lines/second)
Physical Source Lines of Code (SLOC) = 2314
Hits@level = [0]   0 [1]  14 [2]   9 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]  24 [1+]  24 [2+]  10 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 10.3717 [1+] 10.3717 [2+] 4.32152 [3+] 0.432152 [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.