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/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationHash.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationHash.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationHashEntry.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationHashEntry.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationOutputVector.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationOutputVector.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationTempFileGenerator.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationTempFileGenerator.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationVector.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationVector.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollatorInterface.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamCollatorInterface.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamFileDecoder.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamFileDecoder.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamFlagBase.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamHeaderInfo.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamHeaderInfo.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamWriter.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BamWriter.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_CharBuffer.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_CharBuffer.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_Chromosome.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_Chromosome.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_CollatorState.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_FastQRead.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_FormatNumber.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_FormatNumber.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipFileDecoder.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipFileDecoder.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipReader.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipReader.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipWriter.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_GzipWriter.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_Hash.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_Hash.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_LineBuffer.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_LineBuffer.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_LineParsing.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_LineParsing.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_List.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_List.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_ListNode.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_ListNode.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_MergeHeapEntry.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamBamFileDecoder.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamBamFileDecoder.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamFileDecoder.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamFileDecoder.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c
Examining data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.h
Examining data/bambamc-0.0.50/src/bambamc/BamBam_Unused.h
Examining data/bambamc-0.0.50/src/test/bamreadertest.c
Examining data/bambamc-0.0.50/src/test/bamwritertest.c

FINAL RESULTS:

data/bambamc-0.0.50/src/bambamc/BamBam_FormatNumber.c:130:2:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
	snprintf(smem,numlen+1,fs,(unsigned long long)num);
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:595:4:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
			strcpy(saminfo->rnext,saminfo->rname);
data/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.c:110:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static char const cmap[5] = {1,2,4,8,15};
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:667:5:  [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(collator->headerline,s,BamBam_getLineLength(s));
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:694:6:  [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(collator->vn,t+3,(nexttab-t)-3);
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:709:6:  [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(collator->so,t+3,(nexttab-t)-3);					
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:759:7:  [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(sn,t+3,(nexttab-t)-3);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:175:3:  [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(header->headerlines[headerlines],c,len);		
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:210:6:  [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(header->sortorder,d,e-d);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:233:6:  [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(header->version,d,e-d);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:418:7:  [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(sn,c+3,(ce-c)-3);						
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:530:2:  [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 magic[4];
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:531:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static char const expMagic[4] = {'B','A','M',1};
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:588:3:  [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(ztext,header->text,l);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:868:6:  [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(cname,name,namee-name);
data/bambamc-0.0.50/src/bambamc/BamBam_BamHeaderInfo.c:154:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static char const magic[4] = { 'B', 'A', 'M', 1 };
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:397:91:  [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.
uint8_t const * BamBam_BamSingleAlignment_FindAux(BamBam_BamSingleAlignment const * algn, char const tag[2])
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:1263:3:  [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(data->data,block,blocksize);
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:1301:3:  [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(data->data,o->data,data->dataav);
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:1309:3:  [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(data->query,o->query,o->queryspace);
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:1317:3:  [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(data->qual,o->qual,o->qualspace);
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.c:1325:3:  [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(data->cigar,o->cigar,o->cigarspace);
data/bambamc-0.0.50/src/bambamc/BamBam_BamSingleAlignment.h:111:98:  [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 uint8_t const * BamBam_BamSingleAlignment_FindAux(BamBam_BamSingleAlignment const * algn, char const tag[2]);
data/bambamc-0.0.50/src/bambamc/BamBam_BamWriter.c:56:2:  [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 mode[3] = "w1\0";
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:21:14:  [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 const char BamBam_GzipHeaderData[18] =
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:88:4:  [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(object->outbuffer,BamBam_GzipHeaderData,sizeof(BamBam_GzipHeaderData));
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:193:4:  [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(object->inbuffer+object->inbufferfill,data,towrite);
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:241:22:  [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).
	object->closefile = fopen(filename,"wb");
data/bambamc-0.0.50/src/bambamc/BamBam_CharBuffer.c:40:2:  [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(charbuffer->buffer,o->buffer,o->buffersize);
data/bambamc-0.0.50/src/bambamc/BamBam_CharBuffer.c:78:3:  [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(newbuffer,buffer->buffer,buffer->bufferfill);
data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.c:117:2:  [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(opc,alignment->query,seqlen); opc += seqlen; *(opc++) = term;
data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.c:121:2:  [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(opc,alignment->qual,seqlen); opc += seqlen; *(opc++) = term;
data/bambamc-0.0.50/src/bambamc/BamBam_GzipWriter.c:27:2:  [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 modestr[4] = { 'w', 'b', '0', 0 };
data/bambamc-0.0.50/src/bambamc/BamBam_GzipWriter.c:53:2:  [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 modestr[4] = { 'w', 'b', '0', 0 };
data/bambamc-0.0.50/src/bambamc/BamBam_LineBuffer.c:122:7:  [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(tmpbuf,object->bufferptrout,numbytes);
data/bambamc-0.0.50/src/bambamc/BamBam_SamFileDecoder.c:155:22:  [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).
	object->closefile = fopen(filename,"rb");
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:104:3:  [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(*str,field[0],fieldlen);
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:162:8:  [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.
static char BamBam_SamInfo_qnameValid[256];
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:164:8:  [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.
static char BamBam_SamInfo_rnameFirstValid[256];
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:166:8:  [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.
static char BamBam_SamInfo_rnameOtherValid[256];
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:168:8:  [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.
static char BamBam_SamInfo_seqValid[256];
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:170:8:  [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.
static char BamBam_SamInfo_qualValid[256];
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.h:25:9:  [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.
typedef char const * BamBam_SamInfo_cptrpair[2];
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:31:2:  [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(c,s,len);
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:46:2:  [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(c+0   ,sa,lena);
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:47:2:  [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(c+lena,sb,lenb);
data/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.c:104:24:  [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).
	uint64_t const qlen = strlen(query);
data/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.c:106:27:  [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).
	uint64_t const namelen = strlen(name);
data/bambamc-0.0.50/src/bambamc/BamBam_BamAlignmentPut.c:292:11:  [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 ( strlen(tag) == 2 );
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationHashEntry.c:124:24:  [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).
	hashentry->qnamelen = strlen(hashentry->qname);	
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationTempFileGenerator.c:57:3:  [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(prefix) +
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationTempFileGenerator.c:59:3:  [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(spid) +
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollationTempFileGenerator.c:61:3:  [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(sid) +
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:590:19:  [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).
	tempdirnamelen = strlen(tempdirname);
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:591:39:  [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).
	tempfileprefixlen = tempdirnamelen + strlen(tempadd) + 1;
data/bambamc-0.0.50/src/bambamc/BamBam_BamCollator.c:653:35:  [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 ( collator->bamheadertext && (strlen(collator->bamheadertext) != 0) )
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:183:8:  [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 ( strlen(*hc) >= 4 && !strncmp("@HD\t",*hc,4) )
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:319:7:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		c = getc(reader);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:339:9:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				c = getc(reader);
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:386:8:  [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 ( strlen(*hc) >= 4 && !strncmp("@SQ\t",*hc,4) )
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:817:4:  [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(*hc) >= 4 
data/bambamc-0.0.50/src/bambamc/BamBam_BamFileHeader.c:838:13:  [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).
		else if ( strlen(*hc) >= 4 && strncmp("@SQ\t",*hc,4) == 0 )
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:304:23:  [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).
	uint32_t const len = strlen(c);
data/bambamc-0.0.50/src/bambamc/BamBam_BgzfCompressor.c:309:23:  [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).
	uint32_t const len = strlen(c);
data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.c:115:31:  [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).
	opc = BamBam_PutAtLine(qname,strlen(qname),flags,opc,term);
data/bambamc-0.0.50/src/bambamc/BamBam_FormatAlignment.c:130:32:  [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).
	unsigned int const qnamelen = strlen(qname);
data/bambamc-0.0.50/src/bambamc/BamBam_LineParsing.c:84:9:  [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 ( (strlen(filter) == (size_t)(se-sa)) && memcmp(filter,sa,se-sa) == 0 )
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:439:21:  [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).
			if ( exseqlen != strlen(saminfo->seq) )
data/bambamc-0.0.50/src/bambamc/BamBam_SamInfo.c:584:33:  [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).
		unsigned int const rnamelen = strlen(saminfo->rname);
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:25:21:  [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).
	size_t const len = strlen(s);
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:39:22:  [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).
	size_t const lena = strlen(sa);
data/bambamc-0.0.50/src/bambamc/BamBam_StrDup.c:40:22:  [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).
	size_t const lenb = strlen(sb);

ANALYSIS SUMMARY:

Hits = 72
Lines analyzed = 9461 in approximately 0.28 seconds (33938 lines/second)
Physical Source Lines of Code (SLOC) = 6589
Hits@level = [0]  97 [1]  26 [2]  44 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+] 169 [1+]  72 [2+]  46 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 25.6488 [1+] 10.9273 [2+] 6.98133 [3+] 0.303536 [4+] 0.303536 [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.