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/biobambam2-2.0.177+ds/src/biobambam2/AttachRank.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/AttachRank.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ClipAdapters.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ClipAdapters.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ClipReinsert.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ClipReinsert.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/DepthInterval.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/DepthInterval.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/DepthIntervalGetter.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/KmerPoisson.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/KmerPoisson.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Licensing.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Licensing.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ReadHeader.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ReadHeader.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Reference.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ResetAlignment.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/ResetAlignment.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/RgInfo.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/RunEOFFilter.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/RunEOFFilter.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Split12.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Split12.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Strip12.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/Strip12.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/UpdateNumericalIndex.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/UpdateNumericalIndex.hpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/zzToName.cpp
Examining data/biobambam2-2.0.177+ds/src/biobambam2/zzToName.hpp
Examining data/biobambam2-2.0.177+ds/src/programs/bam12auxmerge.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bam12split.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bam12strip.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamadapterclip.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamadapterfind.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamalignfrac.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamauxmerge.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamauxmerge2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamauxsort.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bambisect.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamcat.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamchecksort.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamclipXT.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamclipreinsert.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamcollate2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamconsensus.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamcountflags.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdepth.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdepthintersect.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdepthmerge.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdifference.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdisthist.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamexondepth.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamexplode.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamexploderef.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamexploderg.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfastcat.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfastexploderef.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfastnumextract.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfastsplit.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfeaturecount.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfillquery.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilter.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilteraux.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterbyname.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfiltereofblocks.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterflags.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterheader.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterheader2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterk.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterlength.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfiltermc.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilternames.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterrefid.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfilterrg.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfixmatecoordinates.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfixmatecoordinatesnamesorted.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfixmateinformation.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfixpairinfo.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamflagsplit.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamfrontback.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamheadercat.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamheap2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamheap3.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamindex.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamintervalcomment.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamintervalcommenthist.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammapdist.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesopt.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesoptdist.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammaskflags.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammdnm.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bammerge.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamnumericalindex.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamnumericalindexstats.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrandomtag.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrank.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamranksort.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrecalculatecigar.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrecompress.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrefextract.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamrefinterval.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamreheader.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamreplacechecksums.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamreset.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamscrapcount.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamseqchksum.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamsimpledepth.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamsormadup.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamsort.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamsplit.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamsplitdiv.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamstreamingmarkduplicates.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamtagconversion.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamtofastq.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamtoname.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamzztoname.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/blastnxmltobam.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastabgzfextract.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastaexplod.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastaselectreg.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastqtobam.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastqtobam2.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/fastqtobampar.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/filtergtf.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/normalisefasta.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/populaterefcache.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfconcat.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfdiff.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcffilterfilterflags.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcffilterinfo.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcffiltersamples.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfpatchcontigprepend.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfreplacecontigs.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfreplacecontigsmap.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/vcfsort.cpp
Examining data/biobambam2-2.0.177+ds/src/programs/bamvalidate.cpp
Examining data/biobambam2-2.0.177+ds/test/bamcmp.cpp
Examining data/biobambam2-2.0.177+ds/test/bamtosam.cpp

FINAL RESULTS:

data/biobambam2-2.0.177+ds/src/programs/bambisect.cpp:93:18:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			int const r = system(fullcommand.c_str());
data/biobambam2-2.0.177+ds/src/programs/bamconsensus.cpp:1785:18:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			int const r = system(com.c_str());
data/biobambam2-2.0.177+ds/src/programs/bamconsensus.cpp:2539:18:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			int const r = system(com.c_str());
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:101:35:  [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.
		uint32_t const rv = ::libmaus2::random::Random::rand32();
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:234:13:  [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.
		libmaus2::random::Random::setup(seed);
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:238:13:  [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.
		libmaus2::random::Random::setup();
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:347:13:  [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.
		libmaus2::random::Random::setup(seed);
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:351:13:  [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.
		libmaus2::random::Random::setup();
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:434:47:  [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.
	runSelectionHash(BAD,up,Pout.get(),libmaus2::random::Random::rand32());
data/biobambam2-2.0.177+ds/src/programs/bamrandomtag.cpp:126:2:  [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(time(0));
data/biobambam2-2.0.177+ds/src/programs/bamsormadup.cpp:292:29:  [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.
				char const * refcache = getenv("REF_CACHE");
data/biobambam2-2.0.177+ds/src/programs/normalisefasta.cpp:84:12:  [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.
	libmaus2::random::Random::setup(::time(0));
data/biobambam2-2.0.177+ds/src/programs/normalisefasta.cpp:126:50:  [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.
					s[i] = libmaus2::fastx::remapChar(libmaus2::random::Random::rand8()&3);
data/biobambam2-2.0.177+ds/src/programs/populaterefcache.cpp:32:7:  [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("REF_CACHE") == NULL )
data/biobambam2-2.0.177+ds/src/programs/bambisect.cpp:35:50:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
	std::string const fullcommand = command + " " + tmpfile;
data/biobambam2-2.0.177+ds/src/programs/bambisect.cpp:89:16:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
			BNE.extract(tmpfile,level,S.from,S.to);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates.cpp:531:5:  [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(outptr,tag1,l1);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates.cpp:535:5:  [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(outptr,tag2,l2);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates2.cpp:1561:5:  [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(outptr,tag1,l1);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates2.cpp:1565:5:  [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(outptr,tag2,l2);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesopt.cpp:627:5:  [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(outptr,tag1,l1);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesopt.cpp:631:5:  [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(outptr,tag2,l2);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesoptdist.cpp:698:5:  [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(outptr,tag1,l1);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesoptdist.cpp:702:5:  [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(outptr,tag2,l2);
data/biobambam2-2.0.177+ds/src/programs/blastnxmltobam.cpp:1015:29:  [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).
				uint64_t const offset = atoi(hspQueryFrom.c_str());
data/biobambam2-2.0.177+ds/src/programs/blastnxmltobam.cpp:1044:29:  [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).
				uint64_t const offset = atoi(hspHitFrom.c_str());
data/biobambam2-2.0.177+ds/src/biobambam2/ClipReinsert.cpp:89:75:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			algn.replaceSequence( libmaus2::fastx::reverseComplementUnmapped(qs) + read, std::string(qq.rbegin(),qq.rend()) + qual);
data/biobambam2-2.0.177+ds/src/biobambam2/DepthInterval.hpp:61:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read(
data/biobambam2-2.0.177+ds/src/programs/bam12auxmerge.cpp:62:19:  [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).
	size_t len_str = strlen(str);
data/biobambam2-2.0.177+ds/src/programs/bam12auxmerge.cpp:63:19:  [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).
	size_t len_suf = strlen(suf);
data/biobambam2-2.0.177+ds/src/programs/bamauxmerge2.cpp:860:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					info.stream->read(c,s);
data/biobambam2-2.0.177+ds/src/programs/bamauxmerge2.cpp:1532:29:  [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).
			uint64_t const cliplen = strlen(qs);
data/biobambam2-2.0.177+ds/src/programs/bamauxmerge2.cpp:1534:20:  [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).
			if ( (! qq) || (strlen(qq) != cliplen) )
data/biobambam2-2.0.177+ds/src/programs/bamauxmerge2.cpp:1795:10:  [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).
									strlen(nn)
data/biobambam2-2.0.177+ds/src/programs/bamcollate2.cpp:159:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		CIS.read(ctext.begin(),headerlen);
data/biobambam2-2.0.177+ds/src/programs/bamconsensus.cpp:3395:29:  [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).
			char const * n_e = n_a + strlen(n_a);
data/biobambam2-2.0.177+ds/src/programs/bamconsensus.cpp:3557:30:  [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).
				char const * n_e = n_a + strlen(n_a);
data/biobambam2-2.0.177+ds/src/programs/bamdownsamplerandom.cpp:191:55:  [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).
		dig.update(reinterpret_cast<uint8_t const *>(qname),strlen(qname));
data/biobambam2-2.0.177+ds/src/programs/bamfastexploderef.cpp:144:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
								ISI.read(C.begin(),toread);
data/biobambam2-2.0.177+ds/src/programs/bamfixpairinfo.cpp:153:23:  [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).
			uint64_t const l = strlen(name);
data/biobambam2-2.0.177+ds/src/programs/bamfrontback.cpp:99:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		CIS.read(ctext.begin(),headerlen);
data/biobambam2-2.0.177+ds/src/programs/bamfrontback.cpp:182:29:  [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).
	uint64_t const cfrontlen = strlen(cfront);
data/biobambam2-2.0.177+ds/src/programs/bamfrontback.cpp:184:28:  [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).
	uint64_t const cbacklen = strlen(cback);
data/biobambam2-2.0.177+ds/src/programs/bamfrontback.cpp:205:29:  [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).
					uint64_t const lname = strlen(name);
data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp:60:10:  [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).
uint64_t strlen(std::pair<uint8_t,uint8_t> const * const rp)
data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp:83:23:  [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).
			pairstringfreelist[strlen(insbases[i])+1].push_back(insbases[i]);
data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp:259:31:  [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).
					maxlen = std::max(maxlen,strlen(entry->insbases[i]));
data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp:416:16:  [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).
					acclen += strlen(pendinginserts[i]);
data/biobambam2-2.0.177+ds/src/programs/bamheap.cpp:423:28:  [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).
					uint64_t const llen = strlen(pendinginserts[i]);
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates.cpp:513:18:  [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).
					l1 = tag1 ? strlen(tag1) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates.cpp:519:18:  [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).
					l2 = tag2 ? strlen(tag2) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates2.cpp:1543:18:  [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).
					l1 = tag1 ? strlen(tag1) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicates2.cpp:1549:18:  [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).
					l2 = tag2 ? strlen(tag2) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesopt.cpp:609:18:  [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).
					l1 = tag1 ? strlen(tag1) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesopt.cpp:615:18:  [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).
					l2 = tag2 ? strlen(tag2) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesoptdist.cpp:680:18:  [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).
					l1 = tag1 ? strlen(tag1) : 0;
data/biobambam2-2.0.177+ds/src/programs/bammarkduplicatesoptdist.cpp:686:18:  [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).
					l2 = tag2 ? strlen(tag2) : 0;
data/biobambam2-2.0.177+ds/src/programs/bamrefextract.cpp:54:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read(reinterpret_cast<char *>(&p),4);
data/biobambam2-2.0.177+ds/src/programs/bamrefextract.cpp:55:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read(reinterpret_cast<char *>(&c),1);
data/biobambam2-2.0.177+ds/src/programs/bamreheader.cpp:136:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
						IOSI->read(A.begin(),isize);
data/biobambam2-2.0.177+ds/src/programs/bamreheader.cpp:179:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
						IOSI->read(A.begin(),isize);
data/biobambam2-2.0.177+ds/src/programs/bamreplacechecksums.cpp:161:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
						IOSI->read(A.begin(),isize);
data/biobambam2-2.0.177+ds/src/programs/bamreplacechecksums.cpp:204:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
						IOSI->read(A.begin(),isize);
data/biobambam2-2.0.177+ds/src/programs/bamreset.cpp:99:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		CIS.read(ctext.begin(),headerlen);
data/biobambam2-2.0.177+ds/src/programs/blastnxmltobam.cpp:154:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read(reinterpret_cast<char *>(toFill),maxToRead);
data/biobambam2-2.0.177+ds/src/programs/fastabgzfextract.cpp:95:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				Pstr->read(B.begin(),len);
data/biobambam2-2.0.177+ds/src/programs/fastqtobam2.cpp:1095:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					info.stream->read(c,s);
data/biobambam2-2.0.177+ds/src/programs/filtergtf.cpp:227:24:  [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).
				gene_id = s.substr(strlen("gene_id "));
data/biobambam2-2.0.177+ds/src/programs/filtergtf.cpp:231:30:  [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).
				transcript_id = s.substr(strlen("transcript_id "));
data/biobambam2-2.0.177+ds/src/programs/filtergtf.cpp:235:34:  [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).
				exon_number = parse(s.substr(strlen("exon_number ")));

ANALYSIS SUMMARY:

Hits = 70
Lines analyzed = 55603 in approximately 1.46 seconds (37970 lines/second)
Physical Source Lines of Code (SLOC) = 42665
Hits@level = [0]   0 [1]  44 [2]  12 [3]  11 [4]   3 [5]   0
Hits@level+ = [0+]  70 [1+]  70 [2+]  26 [3+]  14 [4+]   3 [5+]   0
Hits/KSLOC@level+ = [0+] 1.64069 [1+] 1.64069 [2+] 0.609399 [3+] 0.328138 [4+] 0.0703152 [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.