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/bowtie-1.3.0+dfsg1/aligner.h
Examining data/bowtie-1.3.0+dfsg1/aligner_0mm.h
Examining data/bowtie-1.3.0+dfsg1/aligner_1mm.h
Examining data/bowtie-1.3.0+dfsg1/aligner_23mm.h
Examining data/bowtie-1.3.0+dfsg1/aligner_metrics.h
Examining data/bowtie-1.3.0+dfsg1/aligner_seed_mm.h
Examining data/bowtie-1.3.0+dfsg1/alphabet.cpp
Examining data/bowtie-1.3.0+dfsg1/alphabet.h
Examining data/bowtie-1.3.0+dfsg1/assert_helpers.h
Examining data/bowtie-1.3.0+dfsg1/binary_sa_search.h
Examining data/bowtie-1.3.0+dfsg1/bitpack.h
Examining data/bowtie-1.3.0+dfsg1/bitset.h
Examining data/bowtie-1.3.0+dfsg1/blockwise_sa.h
Examining data/bowtie-1.3.0+dfsg1/bowtie_build_main.cpp
Examining data/bowtie-1.3.0+dfsg1/bowtie_inspect.cpp
Examining data/bowtie-1.3.0+dfsg1/bowtie_main.cpp
Examining data/bowtie-1.3.0+dfsg1/bt2_locks.cpp
Examining data/bowtie-1.3.0+dfsg1/bt2_locks.h
Examining data/bowtie-1.3.0+dfsg1/btypes.h
Examining data/bowtie-1.3.0+dfsg1/ccnt_lut.cpp
Examining data/bowtie-1.3.0+dfsg1/chaincat.cpp
Examining data/bowtie-1.3.0+dfsg1/cpu_numa_info.cpp
Examining data/bowtie-1.3.0+dfsg1/cpu_numa_info.h
Examining data/bowtie-1.3.0+dfsg1/diff_sample.h
Examining data/bowtie-1.3.0+dfsg1/ds.h
Examining data/bowtie-1.3.0+dfsg1/ebwt.cpp
Examining data/bowtie-1.3.0+dfsg1/ebwt.h
Examining data/bowtie-1.3.0+dfsg1/ebwt_build.cpp
Examining data/bowtie-1.3.0+dfsg1/ebwt_search.cpp
Examining data/bowtie-1.3.0+dfsg1/ebwt_search.h
Examining data/bowtie-1.3.0+dfsg1/ebwt_search_backtrack.h
Examining data/bowtie-1.3.0+dfsg1/ebwt_search_util.cpp
Examining data/bowtie-1.3.0+dfsg1/ebwt_search_util.h
Examining data/bowtie-1.3.0+dfsg1/edit.cpp
Examining data/bowtie-1.3.0+dfsg1/edit.h
Examining data/bowtie-1.3.0+dfsg1/endian_swap.h
Examining data/bowtie-1.3.0+dfsg1/fast_mutex.h
Examining data/bowtie-1.3.0+dfsg1/filebuf.h
Examining data/bowtie-1.3.0+dfsg1/formats.h
Examining data/bowtie-1.3.0+dfsg1/hit.cpp
Examining data/bowtie-1.3.0+dfsg1/hit.h
Examining data/bowtie-1.3.0+dfsg1/hit_set.cpp
Examining data/bowtie-1.3.0+dfsg1/hit_set.h
Examining data/bowtie-1.3.0+dfsg1/log.cpp
Examining data/bowtie-1.3.0+dfsg1/log.h
Examining data/bowtie-1.3.0+dfsg1/ls.cpp
Examining data/bowtie-1.3.0+dfsg1/ls.h
Examining data/bowtie-1.3.0+dfsg1/mm.h
Examining data/bowtie-1.3.0+dfsg1/multikey_qsort.h
Examining data/bowtie-1.3.0+dfsg1/pat.cpp
Examining data/bowtie-1.3.0+dfsg1/pat.h
Examining data/bowtie-1.3.0+dfsg1/pool.h
Examining data/bowtie-1.3.0+dfsg1/processor_support.h
Examining data/bowtie-1.3.0+dfsg1/qual.cpp
Examining data/bowtie-1.3.0+dfsg1/qual.h
Examining data/bowtie-1.3.0+dfsg1/random_source.h
Examining data/bowtie-1.3.0+dfsg1/random_test.cpp
Examining data/bowtie-1.3.0+dfsg1/range.h
Examining data/bowtie-1.3.0+dfsg1/range_cache.h
Examining data/bowtie-1.3.0+dfsg1/range_chaser.h
Examining data/bowtie-1.3.0+dfsg1/range_source.h
Examining data/bowtie-1.3.0+dfsg1/read.h
Examining data/bowtie-1.3.0+dfsg1/ref_aligner.cpp
Examining data/bowtie-1.3.0+dfsg1/ref_aligner.h
Examining data/bowtie-1.3.0+dfsg1/ref_read.h
Examining data/bowtie-1.3.0+dfsg1/reference.h
Examining data/bowtie-1.3.0+dfsg1/row_chaser.h
Examining data/bowtie-1.3.0+dfsg1/sam.cpp
Examining data/bowtie-1.3.0+dfsg1/sam.h
Examining data/bowtie-1.3.0+dfsg1/search_1mm_phase1.c
Examining data/bowtie-1.3.0+dfsg1/search_1mm_phase2.c
Examining data/bowtie-1.3.0+dfsg1/search_23mm_phase1.c
Examining data/bowtie-1.3.0+dfsg1/search_23mm_phase2.c
Examining data/bowtie-1.3.0+dfsg1/search_23mm_phase3.c
Examining data/bowtie-1.3.0+dfsg1/search_exact.c
Examining data/bowtie-1.3.0+dfsg1/search_globals.h
Examining data/bowtie-1.3.0+dfsg1/search_seeded_phase1.c
Examining data/bowtie-1.3.0+dfsg1/search_seeded_phase2.c
Examining data/bowtie-1.3.0+dfsg1/search_seeded_phase3.c
Examining data/bowtie-1.3.0+dfsg1/search_seeded_phase4.c
Examining data/bowtie-1.3.0+dfsg1/sequence_io.h
Examining data/bowtie-1.3.0+dfsg1/shmem.cpp
Examining data/bowtie-1.3.0+dfsg1/shmem.h
Examining data/bowtie-1.3.0+dfsg1/sstring.h
Examining data/bowtie-1.3.0+dfsg1/str_util.h
Examining data/bowtie-1.3.0+dfsg1/threading.h
Examining data/bowtie-1.3.0+dfsg1/timer.h
Examining data/bowtie-1.3.0+dfsg1/tinythread.cpp
Examining data/bowtie-1.3.0+dfsg1/tinythread.h
Examining data/bowtie-1.3.0+dfsg1/tokenize.h
Examining data/bowtie-1.3.0+dfsg1/util.h
Examining data/bowtie-1.3.0+dfsg1/word_io.h
Examining data/bowtie-1.3.0+dfsg1/zbox.h
Examining data/bowtie-1.3.0+dfsg1/ref_read.cpp

FINAL RESULTS:

data/bowtie-1.3.0+dfsg1/filebuf.h:263:9:  [5] (buffer) gets:
  Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
	size_t gets(char *buf, size_t len) {
data/bowtie-1.3.0+dfsg1/pat.h:524:22:  [5] (buffer) gets:
  Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
	size_t rd = filebuf.gets(buf, buflen);
data/bowtie-1.3.0+dfsg1/ebwt.cpp:43:6:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
	if (access((str + ".1." + gBt2_ext).c_str(), R_OK) == 0) {
data/bowtie-1.3.0+dfsg1/ebwt.cpp:67:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
				if (access((str + ".1." + gBt2_ext).c_str(), R_OK) == 0) {
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:1045:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(fname,"%s/%d",dirname,pid);
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:1061:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(fname,"%s/%d",dirname,pid);
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:1078:4:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
			sprintf(fname,"/proc/%s", ent->d_name);
data/bowtie-1.3.0+dfsg1/bowtie_inspect.cpp:113:17:  [3] (buffer) getopt_long:
  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.
		next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
data/bowtie-1.3.0+dfsg1/ebwt.cpp:64:7:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
			if(getenv("BOWTIE_INDEXES") != NULL) {
data/bowtie-1.3.0+dfsg1/ebwt.cpp:65:18:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
				str = string(getenv("BOWTIE_INDEXES")) + "/" + ebwtFileBase;
data/bowtie-1.3.0+dfsg1/ebwt_build.cpp:214:17:  [3] (buffer) getopt_long:
  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.
		next_option = getopt_long(
data/bowtie-1.3.0+dfsg1/ebwt_build.cpp:590:3:  [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(seed);
data/bowtie-1.3.0+dfsg1/ebwt_build.cpp:610:4:  [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(seed);
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:619:17:  [3] (buffer) getopt_long:
  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.
		next_option = getopt_long(
data/bowtie-1.3.0+dfsg1/fast_mutex.h:97:7:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
      InitializeCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/fast_mutex.h:137:7:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
      EnterCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/tinythread.cpp:61:3:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  InitializeCriticalSection(&mWaitersCountLock);
data/bowtie-1.3.0+dfsg1/tinythread.cpp:82:3:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  EnterCriticalSection(&mWaitersCountLock);
data/bowtie-1.3.0+dfsg1/tinythread.cpp:98:3:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  EnterCriticalSection(&mWaitersCountLock);
data/bowtie-1.3.0+dfsg1/tinythread.cpp:112:3:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  EnterCriticalSection(&mWaitersCountLock);
data/bowtie-1.3.0+dfsg1/tinythread.h:168:7:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
      InitializeCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/tinythread.h:191:7:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
      EnterCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/tinythread.h:257:7:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
      InitializeCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/tinythread.h:283:7:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
      EnterCriticalSection(&mHandle);
data/bowtie-1.3.0+dfsg1/tinythread.h:424:7:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
      EnterCriticalSection(&mWaitersCountLock);
data/bowtie-1.3.0+dfsg1/alphabet.cpp:276:8:  [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.
signed char mask2iupac[16] = {
data/bowtie-1.3.0+dfsg1/alphabet.h:172:15:  [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.
extern signed char mask2iupac[16];
data/bowtie-1.3.0+dfsg1/bitset.h:42:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(newwords, words, oldsz >> 3 /* convert to bytes */);
data/bowtie-1.3.0+dfsg1/bowtie_build_main.cpp:35:6:  [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).
		in.open(file);
data/bowtie-1.3.0+dfsg1/bowtie_build_main.cpp:36:3:  [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[4096];
data/bowtie-1.3.0+dfsg1/bowtie_main.cpp:35:6:  [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).
		in.open(file);
data/bowtie-1.3.0+dfsg1/bowtie_main.cpp:36:3:  [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[4096];
data/bowtie-1.3.0+dfsg1/chaincat.cpp:23:14:  [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 *in = fopen(argv[1], "rb");
data/bowtie-1.3.0+dfsg1/diff_sample.h:868:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(sOrig, sPrimeArr, OFF_SIZE * sPrimeSz);
data/bowtie-1.3.0+dfsg1/ds.h:1770:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(list_, o.list_, cur_ * sizeof(T));
data/bowtie-1.3.0+dfsg1/ds.h:2456:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
data/bowtie-1.3.0+dfsg1/ebwt.cpp:46:5:  [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).
	in.open((str + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
data/bowtie-1.3.0+dfsg1/ebwt.cpp:60:6:  [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).
		in.open((str + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
data/bowtie-1.3.0+dfsg1/ebwt.cpp:70:8:  [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).
				in.open((str + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
data/bowtie-1.3.0+dfsg1/ebwt.h:336:4:  [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).
	f.open(name, std::ios_base::binary | std::ios_base::in);
data/bowtie-1.3.0+dfsg1/ebwt.h:2854:14:  [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).
		if((_in1 = fopen(_in1Str.c_str(), "rb")) == NULL) {
data/bowtie-1.3.0+dfsg1/ebwt.h:2859:14:  [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).
		if((_in2 = fopen(_in2Str.c_str(), "rb")) == NULL) {
data/bowtie-1.3.0+dfsg1/ebwt.h:3394:5:  [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 tmp[OFF_SIZE];
data/bowtie-1.3.0+dfsg1/ebwt.h:3542:11:  [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).
    fin = fopen((instr + ".1." + gEbwt_ext).c_str(),"rb");
data/bowtie-1.3.0+dfsg1/ebwt.h:3557:5:  [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).
	in.open((instr + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
data/bowtie-1.3.0+dfsg1/ebwt_build.cpp:337:15:  [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 *f = fopen(infiles[i].c_str(), "rb");
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:1062:12:  [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* f = fopen(fname,"w");
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:1077:14:  [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 pid = atoi(ent->d_name);
data/bowtie-1.3.0+dfsg1/filebuf.h:452:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(buf, _lastn_buf, _lastn_cur);
data/bowtie-1.3.0+dfsg1/filebuf.h:475:12:  [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).
		int fd = open(filename, O_RDONLY);
data/bowtie-1.3.0+dfsg1/filebuf.h:526:2:  [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      _lastn_buf[LASTN_BUF_SZ]; // buffer of the last N chars dispensed
data/bowtie-1.3.0+dfsg1/filebuf.h:539:10:  [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).
		out_ = fopen(in, "wb");
data/bowtie-1.3.0+dfsg1/filebuf.h:592:2:  [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     buf_[BUF_SZ]; // (large) input buffer
data/bowtie-1.3.0+dfsg1/filebuf.h:610:10:  [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).
		out_ = fopen(out.c_str(), binary ? "wb" : "w");
data/bowtie-1.3.0+dfsg1/filebuf.h:626:10:  [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).
		out_ = fopen(out, binary ? "wb" : "w");
data/bowtie-1.3.0+dfsg1/filebuf.h:650:10:  [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).
		out_ = fopen(out, binary ? "wb" : "w");
data/bowtie-1.3.0+dfsg1/filebuf.h:682:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&buf_[cur_], s.data(), slen);
data/bowtie-1.3.0+dfsg1/filebuf.h:687:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(&buf_[cur_], s.data(), slen);
data/bowtie-1.3.0+dfsg1/filebuf.h:708:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&buf_[cur_], s.toZBuf(), slen);
data/bowtie-1.3.0+dfsg1/filebuf.h:713:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(&buf_[cur_], s.toZBuf(), slen);
data/bowtie-1.3.0+dfsg1/filebuf.h:732:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&buf_[cur_], s, len);
data/bowtie-1.3.0+dfsg1/filebuf.h:737:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(&buf_[cur_], s, len);
data/bowtie-1.3.0+dfsg1/filebuf.h:802:2:  [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        buf_[BUF_SZ]; // (large) input buffer
data/bowtie-1.3.0+dfsg1/multikey_qsort.h:631:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(sOrig, s, OFF_SIZE * slen);
data/bowtie-1.3.0+dfsg1/multikey_qsort.h:1063:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		if(cnts[1] > 0) { memcpy(&s[cur], bkts[0], cnts[1] << (OFF_SIZE/4 + 1)); cur += cnts[1]; }
data/bowtie-1.3.0+dfsg1/multikey_qsort.h:1064:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		if(cnts[2] > 0) { memcpy(&s[cur], bkts[1], cnts[2] << (OFF_SIZE/4 + 1)); cur += cnts[2]; }
data/bowtie-1.3.0+dfsg1/multikey_qsort.h:1065:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		if(cnts[3] > 0) { memcpy(&s[cur], bkts[2], cnts[3] << (OFF_SIZE/4 + 1)); cur += cnts[3]; }
data/bowtie-1.3.0+dfsg1/multikey_qsort.h:1066:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		if(cnts[4] > 0) { memcpy(&s[cur], bkts[3], cnts[4] << (OFF_SIZE/4 + 1)); }
data/bowtie-1.3.0+dfsg1/pat.cpp:245:4:  [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).
			open();
data/bowtie-1.3.0+dfsg1/pat.cpp:278:26:  [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).
void CFilePatternSource::open() {
data/bowtie-1.3.0+dfsg1/pat.cpp:308:11:  [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).
				fp_ = fopen(infiles_[filecur_].c_str(), "rb");
data/bowtie-1.3.0+dfsg1/pat.cpp:336:22:  [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).
			} else if((qfp_ = fopen(qinfiles_[filecur_].c_str(), "rb")) == NULL) {
data/bowtie-1.3.0+dfsg1/pat.cpp:630:3:  [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 cbuf[20];
data/bowtie-1.3.0+dfsg1/pat.cpp:966:3:  [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 cbuf[20];
data/bowtie-1.3.0+dfsg1/pat.cpp:1198:2:  [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 cbuf[20];
data/bowtie-1.3.0+dfsg1/pat.h:304:2:  [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 nametmp_[20];                // temp buffer for constructing name
data/bowtie-1.3.0+dfsg1/pat.h:341:3:  [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).
		open(); // open first file in the list
data/bowtie-1.3.0+dfsg1/pat.h:385:3:  [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).
		open();
data/bowtie-1.3.0+dfsg1/pat.h:408:7:  [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).
	void open();
data/bowtie-1.3.0+dfsg1/pat.h:444:2:  [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 buf_[64*1024]; /// file buffer for sequences
data/bowtie-1.3.0+dfsg1/pat.h:445:2:  [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 qbuf_[64*1024]; /// file buffer for qualities
data/bowtie-1.3.0+dfsg1/pat.h:657:2:  [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 buf_[1024];    /// read buffer
data/bowtie-1.3.0+dfsg1/pat.h:659:2:  [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 name_int_buf_[20]; /// for composing offsets for names
data/bowtie-1.3.0+dfsg1/reference.h:64:12:  [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((f3 = fopen(s3.c_str(), "rb")) == NULL) {
data/bowtie-1.3.0+dfsg1/reference.h:72:12:  [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((f4 = fopen(s4.c_str(), "rb")) ==NULL) {
data/bowtie-1.3.0+dfsg1/reference.h:230:18:  [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 *ftmp = fopen(s4.c_str(), "rb");
data/bowtie-1.3.0+dfsg1/reference.h:265:16:  [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 *f4 = fopen(s4.c_str(), "rb");
data/bowtie-1.3.0+dfsg1/sequence_io.h:24:13:  [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 *in = fopen(sstr_to_cstr(infile), "r");
data/bowtie-1.3.0+dfsg1/sequence_io.h:63:13:  [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 *in = fopen(sstr_to_cstr(infile), "r");
data/bowtie-1.3.0+dfsg1/sstring.h:73:38:  [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 inline size_t sstr_len(const char s[N]) {
data/bowtie-1.3.0+dfsg1/sstring.h:690:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_, b, sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:701:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_, b.c_str(), sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:1152:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_, b, sizeof(uint32_t)*nwords());
data/bowtie-1.3.0+dfsg1/sstring.h:1827:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_, b, sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:2001:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_ + len_, b, sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:2099:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(tmp, cs_, sizeof(T)*len_);
data/bowtie-1.3.0+dfsg1/sstring.h:2103:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(ptmp, printcs_, sizeof(char)*len_);
data/bowtie-1.3.0+dfsg1/sstring.h:2153:2:  [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 buf[1024];
data/bowtie-1.3.0+dfsg1/sstring.h:2355:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_, b, sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:2523:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(cs_ + len_, b, sz * sizeof(T));
data/bowtie-1.3.0+dfsg1/sstring.h:2594:2:  [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 printcs_[S+1]; // +1 so that we have the option of dropping in a terminating "\0"
data/bowtie-1.3.0+dfsg1/sstring.h:2732:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(this->cs_, b, sz);
data/bowtie-1.3.0+dfsg1/sstring.h:3036:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(this->cs_, b, sz);
data/bowtie-1.3.0+dfsg1/sstring.h:3305:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(this->cs_, b, sz);
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:179:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void nextRead(const BTDnaString& read) {
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:184:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		float ent = entropyDna5(read);
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:192:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		const size_t len = read.length();
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:194:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			if((int)read[i] == 4) curNumNs_++;
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:198:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	inline float entropyDna5(const BTDnaString& read) {
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:200:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		size_t readLen = read.length();
data/bowtie-1.3.0+dfsg1/aligner_metrics.h:202:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			int c = (int)read[i];
data/bowtie-1.3.0+dfsg1/ebwt.h:3512:22:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        read_value = fgetc(fin);
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:818:26:  [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(optarg == NULL || strlen(optarg) == 0) {
data/bowtie-1.3.0+dfsg1/ebwt_search.cpp:3433:5:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				getchar();
data/bowtie-1.3.0+dfsg1/filebuf.h:231:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					_inf->read((char*)_buf, BUF_SZ);
data/bowtie-1.3.0+dfsg1/filebuf.h:236:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					_ins->read((char*)_buf, BUF_SZ);
data/bowtie-1.3.0+dfsg1/filebuf.h:483:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		ssize_t r1 = read(fd, &byte1, sizeof(uint8_t));
data/bowtie-1.3.0+dfsg1/filebuf.h:484:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		ssize_t r2 = read(fd, &byte2, sizeof(uint8_t));
data/bowtie-1.3.0+dfsg1/filebuf.h:747:17:  [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).
		writeChars(s, strlen(s));
data/bowtie-1.3.0+dfsg1/ls.cpp:37:25:  [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).
		for(size_t i = 0; i < strlen(t); i++) {
data/bowtie-1.3.0+dfsg1/ls.cpp:59:25:  [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).
		for(size_t i = 0; i < strlen(t); i++) {
data/bowtie-1.3.0+dfsg1/ls.cpp:87:25:  [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).
		for(size_t i = 0; i < strlen(t); i++) {
data/bowtie-1.3.0+dfsg1/ls.cpp:105:25:  [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).
		for(size_t i = 0; i < strlen(t); i++) {
data/bowtie-1.3.0+dfsg1/ls.cpp:123:25:  [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).
		for(size_t i = 0; i < strlen(t); i++) {
data/bowtie-1.3.0+dfsg1/range_source.h:1139:14:  [1] (buffer) equal:
  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.
	static bool equal(const Branch* a, const Branch* b) {
data/bowtie-1.3.0+dfsg1/range_source.h:1203:60:  [1] (buffer) equal:
  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.
		assert(bIsBetter  || branchQ_.top() != b || CostCompare::equal(branchQ_.top(), b));
data/bowtie-1.3.0+dfsg1/range_source.h:1204:60:  [1] (buffer) equal:
  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.
		assert(!bIsBetter || branchQ_.top() == b || CostCompare::equal(branchQ_.top(), b));
data/bowtie-1.3.0+dfsg1/read.h:222:6:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	int getc(TReadOff off5p, bool fw) const {
data/bowtie-1.3.0+dfsg1/ref_read.h:75:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		first = fgetc(in) ? true : false;
data/bowtie-1.3.0+dfsg1/sstring.h:74:10:  [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).
		return strlen(s);
data/bowtie-1.3.0+dfsg1/sstring.h:82:10:  [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).
		return strlen(s);
data/bowtie-1.3.0+dfsg1/sstring.h:90:10:  [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).
		return strlen((const char *)s);
data/bowtie-1.3.0+dfsg1/sstring.h:565:14:  [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).
		install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:708:14:  [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).
		install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:836:34:  [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).
		ASSERT_ONLY(size_t xformElts = strlen(xform));
data/bowtie-1.3.0+dfsg1/sstring.h:970:22:  [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).
				installColors(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:972:21:  [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).
				installChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:975:15:  [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).
			install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1221:14:  [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).
		install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1228:19:  [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).
		installChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1235:20:  [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).
		installColors(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1285:21:  [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).
		installReverse(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1317:26:  [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).
		installReverseChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1349:27:  [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).
		installReverseColors(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1688:14:  [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).
		install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:1835:40:  [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).
	void install(const T* b) { install(b, strlen(b)); }
data/bowtie-1.3.0+dfsg1/sstring.h:2009:13:  [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).
		append(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:2032:34:  [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).
		ASSERT_ONLY(size_t xformElts = strlen(xform));
data/bowtie-1.3.0+dfsg1/sstring.h:2224:14:  [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).
		install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:2362:40:  [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).
	void install(const T* b) { install(b, strlen(b)); }
data/bowtie-1.3.0+dfsg1/sstring.h:2531:13:  [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).
		append(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:2572:34:  [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).
		ASSERT_ONLY(size_t xformElts = strlen(xform));
data/bowtie-1.3.0+dfsg1/sstring.h:2671:22:  [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).
				installColors(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:2673:21:  [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).
				installChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:2676:15:  [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).
			install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:3022:22:  [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).
				installColors(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:3024:21:  [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).
				installChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:3027:15:  [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).
			install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:3241:20:  [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).
			installChars(b, strlen(b));
data/bowtie-1.3.0+dfsg1/sstring.h:3243:15:  [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).
			install(b, strlen(b));
data/bowtie-1.3.0+dfsg1/tinythread.h:704:5:  [1] (obsolete) usleep:
  This C routine is considered obsolete (as opposed to the shell command by
  the same name). The interaction of this function with SIGALRM and other
  timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
  unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
    usleep(int(double(aTime.count()) * (1000000.0 * _Period::_as_double()) + 0.5));
data/bowtie-1.3.0+dfsg1/word_io.h:54:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	in.read((char *)&x, sizeof(T));
data/bowtie-1.3.0+dfsg1/word_io.h:92:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	in.read((char *)&x, sizeof(T));

ANALYSIS SUMMARY:

Hits = 163
Lines analyzed = 52386 in approximately 1.24 seconds (42298 lines/second)
Physical Source Lines of Code (SLOC) = 38830
Hits@level = [0]   9 [1]  59 [2]  79 [3]  18 [4]   5 [5]   2
Hits@level+ = [0+] 172 [1+] 163 [2+] 104 [3+]  25 [4+]   7 [5+]   2
Hits/KSLOC@level+ = [0+] 4.42956 [1+] 4.19779 [2+] 2.67834 [3+] 0.643832 [4+] 0.180273 [5+] 0.0515066
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.