, Index(0)
, HasIndex(false)
, AlignmentsBeginOffset(0)
-// , m_header(0)
+ // , m_header(0)
, IndexCacheMode(BamIndex::LimitedIndexCaching)
, HasAlignmentsInRegion(true)
, Parent(parent)
const int rightBoundRefId = ( region.isRightBoundSpecified() ? region.RightRefID : References.size() - 1 );
while ( currentId <= rightBoundRefId ) {
- HasAlignmentsInRegion = Index->HasAlignments(currentId);
- if ( HasAlignmentsInRegion ) break;
- ++currentId;
+ HasAlignmentsInRegion = Index->HasAlignments(currentId);
+ if ( HasAlignmentsInRegion ) break;
+ ++currentId;
}
// if no data found on any reference in region
// if left bound of desired region had no data, use first reference that had data
// otherwise, leave requested region as-is
if ( currentId != region.LeftRefID ) {
- region.LeftRefID = currentId;
- region.LeftPosition = 0;
+ region.LeftRefID = currentId;
+ region.LeftPosition = 0;
}
}
-// fills out character data for BamAlignment data
-bool BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
-
- // calculate character lengths/offsets
- const unsigned int dataLength = bAlignment.SupportData.BlockLength - BAM_CORE_SIZE;
- const unsigned int seqDataOffset = bAlignment.SupportData.QueryNameLength + (bAlignment.SupportData.NumCigarOperations * 4);
- const unsigned int qualDataOffset = seqDataOffset + (bAlignment.SupportData.QuerySequenceLength+1)/2;
- const unsigned int tagDataOffset = qualDataOffset + bAlignment.SupportData.QuerySequenceLength;
- const unsigned int tagDataLength = dataLength - tagDataOffset;
-
- // check offsets to see what char data exists
- const bool hasSeqData = ( seqDataOffset < dataLength );
- const bool hasQualData = ( qualDataOffset < dataLength );
- const bool hasTagData = ( tagDataOffset < dataLength );
-
- // set up char buffers
- const char* allCharData = bAlignment.SupportData.AllCharData.data();
- const char* seqData = ( hasSeqData ? (((const char*)allCharData) + seqDataOffset) : (const char*)0 );
- const char* qualData = ( hasQualData ? (((const char*)allCharData) + qualDataOffset) : (const char*)0 );
- char* tagData = ( hasTagData ? (((char*)allCharData) + tagDataOffset) : (char*)0 );
-
- // store alignment name (relies on null char in name as terminator)
- bAlignment.Name.assign((const char*)(allCharData));
-
- // save query sequence
- bAlignment.QueryBases.clear();
- if ( hasSeqData ) {
- bAlignment.QueryBases.reserve(bAlignment.SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
- char singleBase = DNA_LOOKUP[ ( (seqData[(i/2)] >> (4*(1-(i%2)))) & 0xf ) ];
- bAlignment.QueryBases.append(1, singleBase);
- }
- }
-
- // save qualities, converting from numeric QV to 'FASTQ-style' ASCII character
- bAlignment.Qualities.clear();
- if ( hasQualData ) {
- bAlignment.Qualities.reserve(bAlignment.SupportData.QuerySequenceLength);
- for (unsigned int i = 0; i < bAlignment.SupportData.QuerySequenceLength; ++i) {
- char singleQuality = (char)(qualData[i]+33);
- bAlignment.Qualities.append(1, singleQuality);
- }
- }
-
- // if QueryBases is empty (and this is a allowed case)
- if ( bAlignment.QueryBases.empty() )
- bAlignment.AlignedBases = bAlignment.QueryBases;
-
- // if QueryBases contains data, then build AlignedBases using CIGAR data
- else {
-
- // resize AlignedBases
- bAlignment.AlignedBases.clear();
- bAlignment.AlignedBases.reserve(bAlignment.SupportData.QuerySequenceLength);
-
- // iterate over CigarOps
- int k = 0;
- vector<CigarOp>::const_iterator cigarIter = bAlignment.CigarData.begin();
- vector<CigarOp>::const_iterator cigarEnd = bAlignment.CigarData.end();
- for ( ; cigarIter != cigarEnd; ++cigarIter ) {
-
- const CigarOp& op = (*cigarIter);
- switch(op.Type) {
-
- case ('M') :
- case ('I') :
- bAlignment.AlignedBases.append(bAlignment.QueryBases.substr(k, op.Length)); // for 'M', 'I' - write bases
- // fall through
-
- case ('S') :
- k += op.Length; // for 'S' - soft clip, skip over query bases
- break;
-
- case ('D') :
- bAlignment.AlignedBases.append(op.Length, '-'); // for 'D' - write gap character
- break;
-
- case ('P') :
- bAlignment.AlignedBases.append( op.Length, '*' ); // for 'P' - write padding character
- break;
-
- case ('N') :
- bAlignment.AlignedBases.append( op.Length, 'N' ); // for 'N' - write N's, skip bases in original query sequence
- break;
-
- case ('H') :
- break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op
-
- default:
- fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here
- exit(1);
- }
- }
- }
-
- // save tag data
- bAlignment.TagData.clear();
- if ( hasTagData ) {
- if ( IsBigEndian ) {
- int i = 0;
- while ( (unsigned int)i < tagDataLength ) {
-
- i += 2; // skip tag type (e.g. "RG", "NM", etc)
- uint8_t type = toupper(tagData[i]); // lower & upper case letters have same meaning
- ++i; // skip value type
-
- switch (type) {
-
- case('A') :
- case('C') :
- ++i;
- break;
-
- case('S') :
- SwapEndian_16p(&tagData[i]);
- i += sizeof(uint16_t);
- break;
-
- case('F') :
- case('I') :
- SwapEndian_32p(&tagData[i]);
- i += sizeof(uint32_t);
- break;
-
- case('D') :
- SwapEndian_64p(&tagData[i]);
- i += sizeof(uint64_t);
- break;
-
- case('H') :
- case('Z') :
- while (tagData[i]) { ++i; }
- ++i; // increment one more for null terminator
- break;
-
- default :
- fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
- exit(1);
- }
- }
- }
-
- // store tagData in alignment
- bAlignment.TagData.resize(tagDataLength);
- memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);
- }
-
- // clear the core-only flag
- bAlignment.SupportData.HasCoreOnly = false;
-
- // return success
- return true;
-}
-
// clear index data structure
void BamReaderPrivate::ClearIndex(void) {
delete Index;
// clear out header data
HeaderText.clear();
-// if ( m_header ) {
-// delete m_header;
-// m_header = 0;
-// }
+
+ // if ( m_header ) {
+ // delete m_header;
+ // m_header = 0;
+ // }
// clear out region flags
Region.clear();
// create index based on type requested
if ( useStandardIndex )
- Index = new BamStandardIndex(&mBGZF, Parent);
+ Index = new BamStandardIndex(&mBGZF, Parent);
else
- Index = new BamToolsIndex(&mBGZF, Parent);
+ Index = new BamToolsIndex(&mBGZF, Parent);
// set index cache mode to full for writing
Index->SetCacheMode(BamIndex::FullIndexCaching);
return HeaderText;
-// if ( m_header )
-// return m_header->Text();
-// else
-// return string("");
+ // if ( m_header )
+ // return m_header->Text();
+ // else
+ // return string("");
}
// get next alignment (from specified region, if given)
// if valid alignment found, attempt to parse char data, and return success/failure
if ( GetNextAlignmentCore(bAlignment) )
- return BuildCharData(bAlignment);
+ return bAlignment.BuildCharData();
// no valid alignment found
else return false;
// if region is set but has no alignments
if ( !Region.isNull() && !HasAlignmentsInRegion )
- return false;
+ return false;
// if valid alignment available
if ( LoadNextAlignment(bAlignment) ) {
- // set core-only flag
- bAlignment.SupportData.HasCoreOnly = true;
+ // set core-only flag
+ bAlignment.SupportData.HasCoreOnly = true;
- // if region not specified with at least a left boundary, return success
- if ( !Region.isLeftBoundSpecified() ) return true;
+ // if region not specified with at least a left boundary, return success
+ if ( !Region.isLeftBoundSpecified() ) return true;
- // determine region state (before, within, after)
- BamReaderPrivate::RegionState state = IsOverlap(bAlignment);
+ // determine region state (before, within, after)
+ BamReaderPrivate::RegionState state = IsOverlap(bAlignment);
- // if alignment lies after region, return false
- if ( state == AFTER_REGION ) return false;
+ // if alignment lies after region, return false
+ if ( state == AFTER_REGION ) return false;
- while ( state != WITHIN_REGION ) {
- // if no valid alignment available (likely EOF) return failure
- if ( !LoadNextAlignment(bAlignment) ) return false;
- // if alignment lies after region, return false (no available read within region)
- state = IsOverlap(bAlignment);
- if ( state == AFTER_REGION ) return false;
- }
+ while ( state != WITHIN_REGION ) {
+ // if no valid alignment available (likely EOF) return failure
+ if ( !LoadNextAlignment(bAlignment) ) return false;
+ // if alignment lies after region, return false (no available read within region)
+ state = IsOverlap(bAlignment);
+ if ( state == AFTER_REGION ) return false;
+ }
- // return success (alignment found that overlaps region)
- return true;
+ // return success (alignment found that overlaps region)
+ return true;
}
// no valid alignment
RefVector::const_iterator refIter = References.begin();
RefVector::const_iterator refEnd = References.end();
for ( ; refIter != refEnd; ++refIter)
- refNames.push_back( (*refIter).RefName );
+ refNames.push_back( (*refIter).RefName );
// return 'index-of' refName ( if not found, returns refNames.size() )
return distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName));
BamReaderPrivate::RegionState BamReaderPrivate::IsOverlap(BamAlignment& bAlignment) {
// if alignment is on any reference sequence before left bound
- if ( bAlignment.RefID < Region.LeftRefID ) return BEFORE_REGION;
+ if ( bAlignment.RefID < Region.LeftRefID )
+ return BEFORE_REGION;
// if alignment starts on left bound reference
else if ( bAlignment.RefID == Region.LeftRefID ) {
- // if alignment starts at or after left boundary
- if ( bAlignment.Position >= Region.LeftPosition) {
-
- // if right boundary is specified AND
- // left/right boundaries are on same reference AND
- // alignment starts past right boundary
- if ( Region.isRightBoundSpecified() &&
- Region.LeftRefID == Region.RightRefID &&
- bAlignment.Position > Region.RightPosition )
- return AFTER_REGION;
-
- // otherwise, alignment is within region
- return WITHIN_REGION;
- }
-
- // alignment starts before left boundary
- else {
- // check if alignment overlaps left boundary
- if ( bAlignment.GetEndPosition() >= Region.LeftPosition ) return WITHIN_REGION;
- else return BEFORE_REGION;
- }
+ // if alignment starts at or after left boundary
+ if ( bAlignment.Position >= Region.LeftPosition) {
+
+ // if right boundary is specified AND
+ // left/right boundaries are on same reference AND
+ // alignment starts past right boundary
+ if ( Region.isRightBoundSpecified() &&
+ Region.LeftRefID == Region.RightRefID &&
+ bAlignment.Position > Region.RightPosition )
+ return AFTER_REGION;
+
+ // otherwise, alignment is within region
+ else
+ return WITHIN_REGION;
+ }
+
+ // alignment starts before left boundary
+ else {
+ // check if alignment overlaps left boundary
+ if ( bAlignment.GetEndPosition() >= Region.LeftPosition )
+ return WITHIN_REGION;
+ else
+ return BEFORE_REGION;
+ }
}
// alignment starts on a reference after the left bound
else {
- // if region has a right boundary
- if ( Region.isRightBoundSpecified() ) {
+ // if region has a right boundary
+ if ( Region.isRightBoundSpecified() ) {
- // alignment is on reference between boundaries
- if ( bAlignment.RefID < Region.RightRefID ) return WITHIN_REGION;
+ // alignment is on reference between boundaries
+ if ( bAlignment.RefID < Region.RightRefID )
+ return WITHIN_REGION;
- // alignment is on reference after right boundary
- else if ( bAlignment.RefID > Region.RightRefID ) return AFTER_REGION;
+ // alignment is on reference after right boundary
+ else if ( bAlignment.RefID > Region.RightRefID )
+ return AFTER_REGION;
- // alignment is on right bound reference
- else {
- // check if alignment starts before or at right boundary
- if ( bAlignment.Position <= Region.RightPosition ) return WITHIN_REGION;
- else return AFTER_REGION;
- }
- }
+ // alignment is on right bound reference
+ else {
+ // check if alignment starts before or at right boundary
+ if ( bAlignment.Position <= Region.RightPosition )
+ return WITHIN_REGION;
+ else
+ return AFTER_REGION;
+ }
+ }
- // otherwise, alignment is after left bound reference, but there is no right boundary
- else return WITHIN_REGION;
+ // otherwise, alignment is after left bound reference, but there is no right boundary
+ else return WITHIN_REGION;
}
}
// load BAM header data
void BamReaderPrivate::LoadHeaderData(void) {
-// m_header = new BamHeader(&mBGZF);
-// bool headerLoadedOk = m_header->Load();
-// if ( !headerLoadedOk )
-// cerr << "BamReader could not load header" << endl;
+ // m_header = new BamHeader(&mBGZF);
+ // bool headerLoadedOk = m_header->Load();
+ // if ( !headerLoadedOk )
+ // cerr << "BamReader could not load header" << endl;
// check to see if proper BAM header
char buffer[4];
if (mBGZF.Read(buffer, 4) != 4) {
- fprintf(stderr, "Could not read header type\n");
- exit(1);
+ fprintf(stderr, "Could not read header type\n");
+ exit(1);
}
if (strncmp(buffer, "BAM\001", 4)) {
- fprintf(stderr, "wrong header type!\n");
- exit(1);
+ fprintf(stderr, "wrong header type!\n");
+ exit(1);
}
// get BAM header text length
// if no index filename provided, so we need to look for available index files
if ( IndexFilename.empty() ) {
- // attempt to load BamIndex based on current Filename provided & preferStandardIndex flag
- const BamIndex::PreferredIndexType type = (preferStandardIndex ? BamIndex::STANDARD : BamIndex::BAMTOOLS);
- Index = BamIndex::FromBamFilename(Filename, &mBGZF, Parent, type);
+ // attempt to load BamIndex based on current Filename provided & preferStandardIndex flag
+ const BamIndex::PreferredIndexType type = (preferStandardIndex ? BamIndex::STANDARD : BamIndex::BAMTOOLS);
+ Index = BamIndex::FromBamFilename(Filename, &mBGZF, Parent, type);
- // if null, return failure
- if ( Index == 0 ) return false;
+ // if null, return failure
+ if ( Index == 0 ) return false;
- // generate proper IndexFilename based on type of index created
- IndexFilename = Filename + Index->Extension();
+ // generate proper IndexFilename based on type of index created
+ IndexFilename = Filename + Index->Extension();
}
else {
- // attempt to load BamIndex based on IndexFilename provided by client
- Index = BamIndex::FromIndexFilename(IndexFilename, &mBGZF, Parent);
+ // attempt to load BamIndex based on IndexFilename provided by client
+ Index = BamIndex::FromIndexFilename(IndexFilename, &mBGZF, Parent);
- // if null, return failure
- if ( Index == 0 ) return false;
+ // if null, return failure
+ if ( Index == 0 ) return false;
}
// set cache mode for BamIndex
// read in core alignment data, make sure the right size of data was read
char x[BAM_CORE_SIZE];
- if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE ) return false;
+ if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE )
+ return false;
if ( IsBigEndian ) {
- for ( int i = 0; i < BAM_CORE_SIZE; i+=sizeof(uint32_t) )
- SwapEndian_32p(&x[i]);
+ for ( int i = 0; i < BAM_CORE_SIZE; i+=sizeof(uint32_t) )
+ SwapEndian_32p(&x[i]);
}
// set BamAlignment 'core' and 'support' data
if ( mBGZF.Read(allCharData, dataLength) == (signed int)dataLength) {
- // store 'allCharData' in supportData structure
- bAlignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength);
+ // store 'allCharData' in supportData structure
+ bAlignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength);
- // set success flag
- readCharDataOK = true;
+ // set success flag
+ readCharDataOK = true;
- // save CIGAR ops
- // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly,
- // even when GetNextAlignmentCore() is called
- const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;
- uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
- CigarOp op;
- bAlignment.CigarData.clear();
- bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);
- for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {
+ // save CIGAR ops
+ // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly,
+ // even when GetNextAlignmentCore() is called
+ const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;
+ uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
+ CigarOp op;
+ bAlignment.CigarData.clear();
+ bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);
+ for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {
- // swap if necessary
- if ( IsBigEndian ) SwapEndian_32(cigarData[i]);
+ // swap if necessary
+ if ( IsBigEndian ) SwapEndian_32(cigarData[i]);
- // build CigarOp structure
- op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
- op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
+ // build CigarOp structure
+ op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);
+ op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];
- // save CigarOp
- bAlignment.CigarData.push_back(op);
- }
+ // save CigarOp
+ bAlignment.CigarData.push_back(op);
+ }
}
free(allCharData);
// iterate over all references in header
for (unsigned int i = 0; i != numberRefSeqs; ++i) {
- // get length of reference name
- mBGZF.Read(buffer, 4);
- unsigned int refNameLength = BgzfData::UnpackUnsignedInt(buffer);
- if ( IsBigEndian ) SwapEndian_32(refNameLength);
- char* refName = (char*)calloc(refNameLength, 1);
-
- // get reference name and reference sequence length
- mBGZF.Read(refName, refNameLength);
- mBGZF.Read(buffer, 4);
- int refLength = BgzfData::UnpackSignedInt(buffer);
- if ( IsBigEndian ) SwapEndian_32(refLength);
-
- // store data for reference
- RefData aReference;
- aReference.RefName = (string)((const char*)refName);
- aReference.RefLength = refLength;
- References.push_back(aReference);
-
- // clean up calloc-ed temp variable
- free(refName);
+ // get length of reference name
+ mBGZF.Read(buffer, 4);
+ unsigned int refNameLength = BgzfData::UnpackUnsignedInt(buffer);
+ if ( IsBigEndian ) SwapEndian_32(refNameLength);
+ char* refName = (char*)calloc(refNameLength, 1);
+
+ // get reference name and reference sequence length
+ mBGZF.Read(refName, refNameLength);
+ mBGZF.Read(buffer, 4);
+ int refLength = BgzfData::UnpackSignedInt(buffer);
+ if ( IsBigEndian ) SwapEndian_32(refLength);
+
+ // store data for reference
+ RefData aReference;
+ aReference.RefName = (string)((const char*)refName);
+ aReference.RefLength = refLength;
+ References.push_back(aReference);
+
+ // clean up calloc-ed temp variable
+ free(refName);
}
}
// mark empty references
for ( int i = 0; i < (int)References.size(); ++i )
- References.at(i).RefHasAlignments = Index->HasAlignments(i);
+ References.at(i).RefHasAlignments = Index->HasAlignments(i);
}
// opens BAM file (and index)
-bool BamReaderPrivate::Open(const string& filename, const string& indexFilename, const bool lookForIndex, const bool preferStandardIndex) {
-
+bool BamReaderPrivate::Open(const string& filename,
+ const string& indexFilename,
+ const bool lookForIndex,
+ const bool preferStandardIndex)
+{
// store filenames
Filename = filename;
IndexFilename = indexFilename;
// if no index filename provided
if ( IndexFilename.empty() ) {
- // client did not specify that index SHOULD be found
- // useful for cases where sequential access is all that is required
- if ( !lookForIndex ) return true;
+ // client did not specify that index SHOULD be found
+ // useful for cases where sequential access is all that is required
+ if ( !lookForIndex ) return true;
- // otherwise, look for index file, return success/fail
- return LoadIndex(lookForIndex, preferStandardIndex) ;
+ // otherwise, look for index file, return success/fail
+ else return LoadIndex(lookForIndex, preferStandardIndex) ;
}
// client supplied an index filename
// (this is useful in a MultiBamReader setting where some BAM files may lack data in regions
// that other BAMs have data)
if ( !HasAlignmentsInRegion ) {
- Region = adjustedRegion;
- return true;
+ Region = adjustedRegion;
+ return true;
}
// attempt jump to user-specified region return false if jump could not be performed at all
projects / bamtools.git / blobdiff