--- /dev/null
+// ***************************************************************************
+// BamStandardIndex.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 25 October 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides index operations for the standardized BAM index format (".bai")
+// ***************************************************************************
+
+#include "api/BamAlignment.h"
+#include "api/internal/bam/BamReader_p.h"
+#include "api/internal/index/BamStandardIndex_p.h"
+#include "api/internal/utils/BamException_p.h"
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <algorithm>
+#include <sstream>
+using namespace std;
+
+// -----------------------------------
+// static BamStandardIndex constants
+// -----------------------------------
+
+const int BamStandardIndex::MAX_BIN = 37450; // =(8^6-1)/7+1
+const int BamStandardIndex::BAM_LIDX_SHIFT = 14;
+const string BamStandardIndex::BAI_EXTENSION = ".bai";
+const char* const BamStandardIndex::BAI_MAGIC = "BAI\1";
+const int BamStandardIndex::SIZEOF_ALIGNMENTCHUNK = sizeof(uint64_t)*2;
+const int BamStandardIndex::SIZEOF_BINCORE = sizeof(uint32_t) + sizeof(int32_t);
+const int BamStandardIndex::SIZEOF_LINEAROFFSET = sizeof(uint64_t);
+
+// ----------------------------
+// RaiiWrapper implementation
+// ----------------------------
+
+BamStandardIndex::RaiiWrapper::RaiiWrapper(void)
+ : IndexStream(0)
+ , Buffer(0)
+{ }
+
+BamStandardIndex::RaiiWrapper::~RaiiWrapper(void) {
+
+ if ( IndexStream ) {
+ fclose(IndexStream);
+ IndexStream = 0;
+ }
+
+ if ( Buffer ) {
+ delete[] Buffer;
+ Buffer = 0;
+ }
+}
+
+// ---------------------------------
+// BamStandardIndex implementation
+// ---------------------------------
+
+// ctor
+BamStandardIndex::BamStandardIndex(Internal::BamReaderPrivate* reader)
+ : BamIndex(reader)
+ , m_bufferLength(0)
+{
+ m_isBigEndian = BamTools::SystemIsBigEndian();
+}
+
+// dtor
+BamStandardIndex::~BamStandardIndex(void) {
+ CloseFile();
+}
+
+void BamStandardIndex::AdjustRegion(const BamRegion& region, uint32_t& begin, uint32_t& end) {
+
+ // retrieve references from reader
+ const RefVector& references = m_reader->GetReferenceData();
+
+ // LeftPosition cannot be greater than or equal to reference length
+ if ( region.LeftPosition >= references.at(region.LeftRefID).RefLength )
+ throw BamException("BamStandardIndex::AdjustRegion", "invalid region requested");
+
+ // set region 'begin'
+ begin = (unsigned int)region.LeftPosition;
+
+ // if right bound specified AND left&right bounds are on same reference
+ // OK to use right bound position as region 'end'
+ if ( region.isRightBoundSpecified() && ( region.LeftRefID == region.RightRefID ) )
+ end = (unsigned int)region.RightPosition;
+
+ // otherwise, set region 'end' to last reference base
+ else end = (unsigned int)references.at(region.LeftRefID).RefLength;
+}
+
+// [begin, end)
+void BamStandardIndex::CalculateCandidateBins(const uint32_t& begin,
+ const uint32_t& end,
+ set<uint16_t>& candidateBins)
+{
+ // initialize list, bin '0' is always a valid bin
+ candidateBins.insert(0);
+
+ // get rest of bins that contain this region
+ unsigned int k;
+ for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { candidateBins.insert(k); }
+ for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { candidateBins.insert(k); }
+ for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { candidateBins.insert(k); }
+ for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { candidateBins.insert(k); }
+ for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { candidateBins.insert(k); }
+}
+
+void BamStandardIndex::CalculateCandidateOffsets(const BaiReferenceSummary& refSummary,
+ const uint64_t& minOffset,
+ set<uint16_t>& candidateBins,
+ vector<int64_t>& offsets)
+{
+ // seek to first bin
+ Seek(refSummary.FirstBinFilePosition, SEEK_SET);
+
+ // iterate over reference bins
+ uint32_t binId;
+ int32_t numAlignmentChunks;
+ set<uint16_t>::iterator candidateBinIter;
+ for ( int i = 0; i < refSummary.NumBins; ++i ) {
+
+ // read bin contents (if successful, alignment chunks are now in m_buffer)
+ ReadBinIntoBuffer(binId, numAlignmentChunks);
+
+ // see if bin is a 'candidate bin'
+ candidateBinIter = candidateBins.find(binId);
+
+ // if not, move on to next bin
+ if ( candidateBinIter == candidateBins.end() )
+ continue;
+
+ // otherwise, check bin's contents against for overlap
+ else {
+
+ size_t offset = 0;
+ uint64_t chunkStart;
+ uint64_t chunkStop;
+
+ // iterate over alignment chunks
+ for ( int j = 0; j < numAlignmentChunks; ++j ) {
+
+ // read chunk start & stop from buffer
+ memcpy((char*)&chunkStart, Resources.Buffer+offset, sizeof(uint64_t));
+ offset += sizeof(uint64_t);
+ memcpy((char*)&chunkStop, Resources.Buffer+offset, sizeof(uint64_t));
+ offset += sizeof(uint64_t);
+
+ // swap endian-ness if necessary
+ if ( m_isBigEndian ) {
+ SwapEndian_64(chunkStart);
+ SwapEndian_64(chunkStop);
+ }
+
+ // store alignment chunk's start offset
+ // if its stop offset is larger than our 'minOffset'
+ if ( chunkStop >= minOffset )
+ offsets.push_back(chunkStart);
+ }
+
+ // 'pop' bin ID from candidate bins set
+ candidateBins.erase(candidateBinIter);
+
+ // quit if no more candidates
+ if ( candidateBins.empty() )
+ break;
+ }
+ }
+}
+
+uint64_t BamStandardIndex::CalculateMinOffset(const BaiReferenceSummary& refSummary,
+ const uint32_t& begin)
+{
+ // if no linear offsets exist, return 0
+ if ( refSummary.NumLinearOffsets == 0 )
+ return 0;
+
+ // if 'begin' starts beyond last linear offset, use the last linear offset as minimum
+ // else use the offset corresponding to the requested start position
+ const int shiftedBegin = begin>>BamStandardIndex::BAM_LIDX_SHIFT;
+ if ( shiftedBegin >= refSummary.NumLinearOffsets )
+ return LookupLinearOffset( refSummary, refSummary.NumLinearOffsets-1 );
+ else
+ return LookupLinearOffset( refSummary, shiftedBegin );
+}
+
+void BamStandardIndex::CheckBufferSize(char*& buffer,
+ unsigned int& bufferLength,
+ const unsigned int& requestedBytes)
+{
+ try {
+ if ( requestedBytes > bufferLength ) {
+ bufferLength = requestedBytes + 10;
+ delete[] buffer;
+ buffer = new char[bufferLength];
+ }
+ } catch ( std::bad_alloc& ) {
+ stringstream s("");
+ s << "out of memory when allocating " << requestedBytes << " bytes";
+ throw BamException("BamStandardIndex::CheckBufferSize", s.str());
+ }
+}
+
+void BamStandardIndex::CheckBufferSize(unsigned char*& buffer,
+ unsigned int& bufferLength,
+ const unsigned int& requestedBytes)
+{
+ try {
+ if ( requestedBytes > bufferLength ) {
+ bufferLength = requestedBytes + 10;
+ delete[] buffer;
+ buffer = new unsigned char[bufferLength];
+ }
+ } catch ( std::bad_alloc& ) {
+ stringstream s("");
+ s << "out of memory when allocating " << requestedBytes << " bytes";
+ throw BamException("BamStandardIndex::CheckBufferSize", s.str());
+ }
+}
+
+void BamStandardIndex::CheckMagicNumber(void) {
+
+ // check 'magic number' to see if file is BAI index
+ char magic[4];
+ const size_t elementsRead = fread(magic, sizeof(char), 4, Resources.IndexStream);
+ if ( elementsRead != 4 )
+ throw BamException("BamStandardIndex::CheckMagicNumber", "could not read BAI magic number");
+
+ // compare to expected value
+ if ( strncmp(magic, BamStandardIndex::BAI_MAGIC, 4) != 0 )
+ throw BamException("BamStandardIndex::CheckMagicNumber", "invalid BAI magic number");
+}
+
+void BamStandardIndex::ClearReferenceEntry(BaiReferenceEntry& refEntry) {
+ refEntry.ID = -1;
+ refEntry.Bins.clear();
+ refEntry.LinearOffsets.clear();
+}
+
+void BamStandardIndex::CloseFile(void) {
+
+ // close file stream
+ if ( IsFileOpen() ) {
+ fclose(Resources.IndexStream);
+ Resources.IndexStream = 0;
+ }
+
+ // clear index file summary data
+ m_indexFileSummary.clear();
+
+ // clean up I/O buffer
+ delete[] Resources.Buffer;
+ Resources.Buffer = 0;
+ m_bufferLength = 0;
+}
+
+// builds index from associated BAM file & writes out to index file
+bool BamStandardIndex::Create(void) {
+
+ // skip if BamReader is invalid or not open
+ if ( m_reader == 0 || !m_reader->IsOpen() ) {
+ SetErrorString("BamStandardIndex::Create", "could not create index: reader is not open");
+ return false;
+ }
+
+ // rewind BamReader
+ if ( !m_reader->Rewind() ) {
+ const string readerError = m_reader->GetErrorString();
+ const string message = "could not create index: \n\t" + readerError;
+ SetErrorString("BamStandardIndex::Create", message);
+ return false;
+ }
+
+ try {
+
+ // open new index file (read & write)
+ string indexFilename = m_reader->Filename() + Extension();
+ OpenFile(indexFilename, "w+b");
+
+ // initialize BaiFileSummary with number of references
+ const int& numReferences = m_reader->GetReferenceCount();
+ ReserveForSummary(numReferences);
+
+ // initialize output file
+ WriteHeader();
+
+ // set up bin, ID, offset, & coordinate markers
+ const uint32_t defaultValue = 0xffffffffu;
+ uint32_t currentBin = defaultValue;
+ uint32_t lastBin = defaultValue;
+ int32_t currentRefID = defaultValue;
+ int32_t lastRefID = defaultValue;
+ uint64_t currentOffset = (uint64_t)m_reader->Tell();
+ uint64_t lastOffset = currentOffset;
+ int32_t lastPosition = defaultValue;
+
+ // iterate through alignments in BAM file
+ BamAlignment al;
+ BaiReferenceEntry refEntry;
+ while ( m_reader->LoadNextAlignment(al) ) {
+
+ // changed to new reference
+ if ( lastRefID != al.RefID ) {
+
+ // if not first reference, save previous reference data
+ if ( lastRefID != (int32_t)defaultValue ) {
+
+ SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset);
+ WriteReferenceEntry(refEntry);
+ ClearReferenceEntry(refEntry);
+
+ // write any empty references between (but *NOT* including) lastRefID & al.RefID
+ for ( int i = lastRefID+1; i < al.RefID; ++i ) {
+ BaiReferenceEntry emptyEntry(i);
+ WriteReferenceEntry(emptyEntry);
+ }
+
+ // update bin markers
+ currentOffset = lastOffset;
+ currentBin = al.Bin;
+ lastBin = al.Bin;
+ currentRefID = al.RefID;
+ }
+
+ // otherwise, this is first pass
+ // be sure to write any empty references up to (but *NOT* including) current RefID
+ else {
+ for ( int i = 0; i < al.RefID; ++i ) {
+ BaiReferenceEntry emptyEntry(i);
+ WriteReferenceEntry(emptyEntry);
+ }
+ }
+
+ // update reference markers
+ refEntry.ID = al.RefID;
+ lastRefID = al.RefID;
+ lastBin = defaultValue;
+ }
+
+ // if lastPosition greater than current alignment position - file not sorted properly
+ else if ( lastPosition > al.Position ) {
+ stringstream s("");
+ s << "BAM file is not properly sorted by coordinate" << endl
+ << "Current alignment position: " << al.Position
+ << " < previous alignment position: " << lastPosition
+ << " on reference ID: " << al.RefID << endl;
+ SetErrorString("BamStandardIndex::Create", s.str());
+ return false;
+ }
+
+ // if alignment's ref ID is valid & its bin is not a 'leaf'
+ if ( (al.RefID >= 0) && (al.Bin < 4681) )
+ SaveLinearOffsetEntry(refEntry.LinearOffsets, al.Position, al.GetEndPosition(), lastOffset);
+
+ // changed to new BAI bin
+ if ( al.Bin != lastBin ) {
+
+ // if not first bin on reference, save previous bin data
+ if ( currentBin != defaultValue )
+ SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset);
+
+ // update markers
+ currentOffset = lastOffset;
+ currentBin = al.Bin;
+ lastBin = al.Bin;
+ currentRefID = al.RefID;
+
+ // if invalid RefID, break out
+ if ( currentRefID < 0 )
+ break;
+ }
+
+ // make sure that current file pointer is beyond lastOffset
+ if ( m_reader->Tell() <= (int64_t)lastOffset ) {
+ SetErrorString("BamStandardIndex::Create", "calculating offsets failed");
+ return false;
+ }
+
+ // update lastOffset & lastPosition
+ lastOffset = m_reader->Tell();
+ lastPosition = al.Position;
+ }
+
+ // after finishing alignments, if any data was read, check:
+ if ( currentRefID >= 0 ) {
+
+ // store last alignment chunk to its bin, then write last reference entry with data
+ SaveAlignmentChunkToBin(refEntry.Bins, currentBin, currentOffset, lastOffset);
+ WriteReferenceEntry(refEntry);
+
+ // then write any empty references remaining at end of file
+ for ( int i = currentRefID+1; i < numReferences; ++i ) {
+ BaiReferenceEntry emptyEntry(i);
+ WriteReferenceEntry(emptyEntry);
+ }
+ }
+
+ } catch ( BamException& e) {
+ m_errorString = e.what();
+ return false;
+ }
+
+ // rewind BamReader
+ if ( !m_reader->Rewind() ) {
+ const string readerError = m_reader->GetErrorString();
+ const string message = "could not create index: \n\t" + readerError;
+ SetErrorString("BamStandardIndex::Create", message);
+ return false;
+ }
+
+ // return success
+ return true;
+}
+
+// returns format's file extension
+const string BamStandardIndex::Extension(void) {
+ return BamStandardIndex::BAI_EXTENSION;
+}
+
+void BamStandardIndex::GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion) {
+
+ // cannot calculate offsets if unknown/invalid reference ID requested
+ if ( region.LeftRefID < 0 || region.LeftRefID >= (int)m_indexFileSummary.size() )
+ throw BamException("BamStandardIndex::GetOffset", "invalid reference ID requested");
+
+ // retrieve index summary for left bound reference
+ const BaiReferenceSummary& refSummary = m_indexFileSummary.at(region.LeftRefID);
+
+ // set up region boundaries based on actual BamReader data
+ uint32_t begin;
+ uint32_t end;
+ AdjustRegion(region, begin, end);
+
+ // retrieve all candidate bin IDs for region
+ set<uint16_t> candidateBins;
+ CalculateCandidateBins(begin, end, candidateBins);
+
+ // use reference's linear offsets to calculate the minimum offset
+ // that must be considered to find overlap
+ const uint64_t& minOffset = CalculateMinOffset(refSummary, begin);
+
+ // attempt to use reference summary, minOffset, & candidateBins to calculate offsets
+ // no data should not be error, just bail
+ vector<int64_t> offsets;
+ CalculateCandidateOffsets(refSummary, minOffset, candidateBins, offsets);
+ if ( offsets.empty() )
+ return;
+
+ // ensure that offsets are sorted before processing
+ sort( offsets.begin(), offsets.end() );
+
+ // binary search for an overlapping block (may not be first one though)
+ BamAlignment al;
+ typedef vector<int64_t>::const_iterator OffsetConstIterator;
+ OffsetConstIterator offsetFirst = offsets.begin();
+ OffsetConstIterator offsetIter = offsetFirst;
+ OffsetConstIterator offsetLast = offsets.end();
+ iterator_traits<OffsetConstIterator>::difference_type count = distance(offsetFirst, offsetLast);
+ iterator_traits<OffsetConstIterator>::difference_type step;
+ while ( count > 0 ) {
+ offsetIter = offsetFirst;
+ step = count/2;
+ advance(offsetIter, step);
+
+ // attempt seek to candidate offset
+ const int64_t& candidateOffset = (*offsetIter);
+ if ( !m_reader->Seek(candidateOffset) ) {
+ const string readerError = m_reader->GetErrorString();
+ const string message = "could not seek in BAM file: \n\t" + readerError;
+ throw BamException("BamToolsIndex::GetOffset", message);
+ }
+
+ // load first available alignment, setting flag to true if data exists
+ *hasAlignmentsInRegion = m_reader->LoadNextAlignment(al);
+
+ // check alignment against region
+ if ( al.GetEndPosition() <= region.LeftPosition ) {
+ offsetFirst = ++offsetIter;
+ count -= step+1;
+ } else count = step;
+ }
+
+ // step back to the offset before the 'current offset' (to make sure we cover overlaps)
+ if ( offsetIter != offsets.begin() )
+ --offsetIter;
+ offset = (*offsetIter);
+}
+
+// returns whether reference has alignments or no
+bool BamStandardIndex::HasAlignments(const int& referenceID) const {
+ if ( referenceID < 0 || referenceID >= (int)m_indexFileSummary.size() )
+ return false;
+ const BaiReferenceSummary& refSummary = m_indexFileSummary.at(referenceID);
+ return ( refSummary.NumBins > 0 );
+}
+
+bool BamStandardIndex::IsFileOpen(void) const {
+ return ( Resources.IndexStream != 0 );
+}
+
+// attempts to use index data to jump to @region, returns success/fail
+// a "successful" jump indicates no error, but not whether this region has data
+// * thus, the method sets a flag to indicate whether there are alignments
+// available after the jump position
+bool BamStandardIndex::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) {
+
+ // clear out flag
+ *hasAlignmentsInRegion = false;
+
+ // skip if invalid reader or not open
+ if ( m_reader == 0 || !m_reader->IsOpen() ) {
+ SetErrorString("BamStandardIndex::Jump", "could not jump: reader is not open");
+ return false;
+ }
+
+ // calculate nearest offset to jump to
+ int64_t offset;
+ try {
+ GetOffset(region, offset, hasAlignmentsInRegion);
+ } catch ( BamException& e ) {
+ m_errorString = e.what();
+ return false;
+ }
+
+ // if region has alignments, return success/fail of seeking there
+ if ( *hasAlignmentsInRegion )
+ return m_reader->Seek(offset);
+
+ // otherwise, simply return true (but hasAlignmentsInRegion flag has been set to false)
+ // (this is OK, BamReader will check this flag before trying to load data)
+ return true;
+}
+
+// loads existing data from file into memory
+bool BamStandardIndex::Load(const std::string& filename) {
+
+ try {
+
+ // attempt to open file (read-only)
+ OpenFile(filename, "rb");
+
+ // validate format
+ CheckMagicNumber();
+
+ // load in-memory summary of index data
+ SummarizeIndexFile();
+
+ // return success
+ return true;
+
+ } catch ( BamException& e ) {
+ m_errorString = e.what();
+ return false;
+ }
+}
+
+uint64_t BamStandardIndex::LookupLinearOffset(const BaiReferenceSummary& refSummary, const int& index) {
+
+ // attempt seek to proper index file position
+ const int64_t linearOffsetFilePosition = (int64_t)refSummary.FirstLinearOffsetFilePosition +
+ index*BamStandardIndex::SIZEOF_LINEAROFFSET;
+ Seek(linearOffsetFilePosition, SEEK_SET);
+
+ // read linear offset from BAI file
+ uint64_t linearOffset;
+ ReadLinearOffset(linearOffset);
+ return linearOffset;
+}
+
+void BamStandardIndex::MergeAlignmentChunks(BaiAlignmentChunkVector& chunks) {
+
+ // skip if chunks are empty, nothing to merge
+ if ( chunks.empty() )
+ return;
+
+ // set up merged alignment chunk container
+ BaiAlignmentChunkVector mergedChunks;
+ mergedChunks.push_back( chunks[0] );
+
+ // iterate over chunks
+ int i = 0;
+ BaiAlignmentChunkVector::iterator chunkIter = chunks.begin();
+ BaiAlignmentChunkVector::iterator chunkEnd = chunks.end();
+ for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) {
+
+ // get 'currentMergeChunk' based on numeric index
+ BaiAlignmentChunk& currentMergeChunk = mergedChunks[i];
+
+ // get sourceChunk based on source vector iterator
+ BaiAlignmentChunk& sourceChunk = (*chunkIter);
+
+ // if currentMergeChunk ends where sourceChunk starts, then merge the two
+ if ( currentMergeChunk.Stop>>16 == sourceChunk.Start>>16 )
+ currentMergeChunk.Stop = sourceChunk.Stop;
+
+ // otherwise
+ else {
+ // append sourceChunk after currentMergeChunk
+ mergedChunks.push_back(sourceChunk);
+
+ // update i, so the next iteration will consider the
+ // recently-appended sourceChunk as new mergeChunk candidate
+ ++i;
+ }
+ }
+
+ // saved newly-merged chunks into (parameter) chunks
+ chunks = mergedChunks;
+}
+
+void BamStandardIndex::OpenFile(const std::string& filename, const char* mode) {
+
+ // make sure any previous index file is closed
+ CloseFile();
+
+ // attempt to open file
+ Resources.IndexStream = fopen(filename.c_str(), mode);
+ if ( !IsFileOpen() ) {
+ const string message = string("could not open file: ") + filename;
+ throw BamException("BamStandardIndex::OpenFile", message);
+ }
+}
+
+void BamStandardIndex::ReadBinID(uint32_t& binId) {
+ const size_t elementsRead = fread(&binId, sizeof(binId), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_32(binId);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadBinID", "could not read BAI bin ID");
+}
+
+void BamStandardIndex::ReadBinIntoBuffer(uint32_t& binId, int32_t& numAlignmentChunks) {
+
+ // read bin header
+ ReadBinID(binId);
+ ReadNumAlignmentChunks(numAlignmentChunks);
+
+ // read bin contents
+ const unsigned int bytesRequested = numAlignmentChunks*BamStandardIndex::SIZEOF_ALIGNMENTCHUNK;
+ ReadIntoBuffer(bytesRequested);
+}
+
+void BamStandardIndex::ReadIntoBuffer(const unsigned int& bytesRequested) {
+
+ // ensure that our buffer is big enough for request
+ BamStandardIndex::CheckBufferSize(Resources.Buffer, m_bufferLength, bytesRequested);
+
+ // read from BAI file stream
+ const size_t bytesRead = fread( Resources.Buffer, sizeof(char), bytesRequested, Resources.IndexStream );
+ if ( bytesRead != (size_t)bytesRequested ) {
+ stringstream s("");
+ s << "expected to read: " << bytesRequested << " bytes, "
+ << "but instead read: " << bytesRead;
+ throw BamException("BamStandardIndex::ReadIntoBuffer", s.str());
+ }
+}
+
+void BamStandardIndex::ReadLinearOffset(uint64_t& linearOffset) {
+ const size_t elementsRead = fread(&linearOffset, sizeof(linearOffset), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_64(linearOffset);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadLinearOffset", "could not read BAI linear offset");
+}
+
+void BamStandardIndex::ReadNumAlignmentChunks(int& numAlignmentChunks) {
+ const size_t elementsRead = fread(&numAlignmentChunks, sizeof(numAlignmentChunks), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_32(numAlignmentChunks);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadNumAlignmentChunks", "could not read BAI chunk count");
+}
+
+void BamStandardIndex::ReadNumBins(int& numBins) {
+ const size_t elementsRead = fread(&numBins, sizeof(numBins), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_32(numBins);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadNumBins", "could not read BAI bin count");
+}
+
+void BamStandardIndex::ReadNumLinearOffsets(int& numLinearOffsets) {
+ const size_t elementsRead = fread(&numLinearOffsets, sizeof(numLinearOffsets), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_32(numLinearOffsets);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadNumAlignmentChunks", "could not read BAI linear offset count");
+}
+
+void BamStandardIndex::ReadNumReferences(int& numReferences) {
+ const size_t elementsRead = fread(&numReferences, sizeof(numReferences), 1, Resources.IndexStream);
+ if ( m_isBigEndian ) SwapEndian_32(numReferences);
+ if ( elementsRead != 1 )
+ throw BamException("BamStandardIndex::ReadNumReferences", "could not read reference count");
+}
+
+void BamStandardIndex::ReserveForSummary(const int& numReferences) {
+ m_indexFileSummary.clear();
+ m_indexFileSummary.assign( numReferences, BaiReferenceSummary() );
+}
+
+void BamStandardIndex::SaveAlignmentChunkToBin(BaiBinMap& binMap,
+ const uint32_t& currentBin,
+ const uint64_t& currentOffset,
+ const uint64_t& lastOffset)
+{
+ // create new alignment chunk
+ BaiAlignmentChunk newChunk(currentOffset, lastOffset);
+
+ // if no entry exists yet for this bin, create one and store alignment chunk
+ BaiBinMap::iterator binIter = binMap.find(currentBin);
+ if ( binIter == binMap.end() ) {
+ BaiAlignmentChunkVector newChunks;
+ newChunks.push_back(newChunk);
+ binMap.insert( pair<uint32_t, BaiAlignmentChunkVector>(currentBin, newChunks));
+ }
+
+ // otherwise, just append alignment chunk
+ else {
+ BaiAlignmentChunkVector& binChunks = (*binIter).second;
+ binChunks.push_back( newChunk );
+ }
+}
+
+void BamStandardIndex::SaveBinsSummary(const int& refId, const int& numBins) {
+ BaiReferenceSummary& refSummary = m_indexFileSummary.at(refId);
+ refSummary.NumBins = numBins;
+ refSummary.FirstBinFilePosition = Tell();
+}
+
+void BamStandardIndex::SaveLinearOffsetEntry(BaiLinearOffsetVector& offsets,
+ const int& alignmentStartPosition,
+ const int& alignmentStopPosition,
+ const uint64_t& lastOffset)
+{
+ // get converted offsets
+ const int beginOffset = alignmentStartPosition >> BamStandardIndex::BAM_LIDX_SHIFT;
+ const int endOffset = (alignmentStopPosition - 1) >> BamStandardIndex::BAM_LIDX_SHIFT;
+
+ // resize vector if necessary
+ int oldSize = offsets.size();
+ int newSize = endOffset + 1;
+ if ( oldSize < newSize )
+ offsets.resize(newSize, 0);
+
+ // store offset
+ for( int i = beginOffset + 1; i <= endOffset; ++i ) {
+ if ( offsets[i] == 0 )
+ offsets[i] = lastOffset;
+ }
+}
+
+void BamStandardIndex::SaveLinearOffsetsSummary(const int& refId, const int& numLinearOffsets) {
+ BaiReferenceSummary& refSummary = m_indexFileSummary.at(refId);
+ refSummary.NumLinearOffsets = numLinearOffsets;
+ refSummary.FirstLinearOffsetFilePosition = Tell();
+}
+
+// seek to position in index file stream
+void BamStandardIndex::Seek(const int64_t& position, const int& origin) {
+ if ( fseek64(Resources.IndexStream, position, origin) != 0 )
+ throw BamException("BamStandardIndex::Seek", "could not seek in BAI file");
+}
+
+void BamStandardIndex::SkipBins(const int& numBins) {
+ uint32_t binId;
+ int32_t numAlignmentChunks;
+ for (int i = 0; i < numBins; ++i)
+ ReadBinIntoBuffer(binId, numAlignmentChunks); // results & buffer ignored
+}
+
+void BamStandardIndex::SkipLinearOffsets(const int& numLinearOffsets) {
+ const unsigned int bytesRequested = numLinearOffsets*BamStandardIndex::SIZEOF_LINEAROFFSET;
+ ReadIntoBuffer(bytesRequested);
+}
+
+void BamStandardIndex::SortLinearOffsets(BaiLinearOffsetVector& linearOffsets) {
+ sort( linearOffsets.begin(), linearOffsets.end() );
+}
+
+void BamStandardIndex::SummarizeBins(BaiReferenceSummary& refSummary) {
+
+ // load number of bins
+ int numBins;
+ ReadNumBins(numBins);
+
+ // store bins summary for this reference
+ refSummary.NumBins = numBins;
+ refSummary.FirstBinFilePosition = Tell();
+
+ // skip this reference's bins
+ SkipBins(numBins);
+}
+
+void BamStandardIndex::SummarizeIndexFile(void) {
+
+ // load number of reference sequences
+ int numReferences;
+ ReadNumReferences(numReferences);
+
+ // initialize file summary data
+ ReserveForSummary(numReferences);
+
+ // iterate over reference entries
+ BaiFileSummary::iterator summaryIter = m_indexFileSummary.begin();
+ BaiFileSummary::iterator summaryEnd = m_indexFileSummary.end();
+ for ( int i = 0; summaryIter != summaryEnd; ++summaryIter, ++i )
+ SummarizeReference(*summaryIter);
+}
+
+void BamStandardIndex::SummarizeLinearOffsets(BaiReferenceSummary& refSummary) {
+
+ // load number of linear offsets
+ int numLinearOffsets;
+ ReadNumLinearOffsets(numLinearOffsets);
+
+ // store bin summary data for this reference
+ refSummary.NumLinearOffsets = numLinearOffsets;
+ refSummary.FirstLinearOffsetFilePosition = Tell();
+
+ // skip linear offsets in index file
+ SkipLinearOffsets(numLinearOffsets);
+}
+
+void BamStandardIndex::SummarizeReference(BaiReferenceSummary& refSummary) {
+ SummarizeBins(refSummary);
+ SummarizeLinearOffsets(refSummary);
+}
+
+// return position of file pointer in index file stream
+int64_t BamStandardIndex::Tell(void) const {
+ return ftell64(Resources.IndexStream);
+}
+
+void BamStandardIndex::WriteAlignmentChunk(const BaiAlignmentChunk& chunk) {
+
+ // localize alignment chunk offsets
+ uint64_t start = chunk.Start;
+ uint64_t stop = chunk.Stop;
+
+ // swap endian-ness if necessary
+ if ( m_isBigEndian ) {
+ SwapEndian_64(start);
+ SwapEndian_64(stop);
+ }
+
+ // write to index file
+ size_t elementsWritten = 0;
+ elementsWritten += fwrite(&start, sizeof(start), 1, Resources.IndexStream);
+ elementsWritten += fwrite(&stop, sizeof(stop), 1, Resources.IndexStream);
+ if ( elementsWritten != 2 )
+ throw BamException("BamStandardIndex::WriteAlignmentChunk", "could not write BAI alignment chunk");
+}
+
+void BamStandardIndex::WriteAlignmentChunks(BaiAlignmentChunkVector& chunks) {
+
+ // make sure chunks are merged (simplified) before writing & saving summary
+ MergeAlignmentChunks(chunks);
+
+ // write chunks
+ int32_t chunkCount = chunks.size();
+ if ( m_isBigEndian ) SwapEndian_32(chunkCount);
+ const size_t elementsWritten = fwrite(&chunkCount, sizeof(chunkCount), 1, Resources.IndexStream);
+ if ( elementsWritten != 1 )
+ throw BamException("BamStandardIndex::WriteAlignmentChunks", "could not write BAI chunk count");
+
+ // iterate over chunks
+ BaiAlignmentChunkVector::const_iterator chunkIter = chunks.begin();
+ BaiAlignmentChunkVector::const_iterator chunkEnd = chunks.end();
+ for ( ; chunkIter != chunkEnd; ++chunkIter )
+ WriteAlignmentChunk( (*chunkIter) );
+}
+
+void BamStandardIndex::WriteBin(const uint32_t& binId, BaiAlignmentChunkVector& chunks) {
+
+ // write BAM bin ID
+ uint32_t binKey = binId;
+ if ( m_isBigEndian ) SwapEndian_32(binKey);
+ const size_t elementsWritten = fwrite(&binKey, sizeof(binKey), 1, Resources.IndexStream);
+ if ( elementsWritten != 1 )
+ throw BamException("BamStandardIndex::WriteBin", "could not write bin ID");
+
+ // write bin's alignment chunks
+ WriteAlignmentChunks(chunks);
+}
+
+void BamStandardIndex::WriteBins(const int& refId, BaiBinMap& bins) {
+
+ // write number of bins
+ int32_t binCount = bins.size();
+ if ( m_isBigEndian ) SwapEndian_32(binCount);
+ const size_t elementsWritten = fwrite(&binCount, sizeof(binCount), 1, Resources.IndexStream);
+ if ( elementsWritten != 1 )
+ throw BamException("BamStandardIndex::WriteBins", "could not write bin count");
+
+ // save summary for reference's bins
+ SaveBinsSummary(refId, bins.size());
+
+ // iterate over bins
+ BaiBinMap::iterator binIter = bins.begin();
+ BaiBinMap::iterator binEnd = bins.end();
+ for ( ; binIter != binEnd; ++binIter )
+ WriteBin( (*binIter).first, (*binIter).second );
+}
+
+void BamStandardIndex::WriteHeader(void) {
+
+ size_t elementsWritten = 0;
+
+ // write magic number
+ elementsWritten += fwrite(BamStandardIndex::BAI_MAGIC, sizeof(char), 4, Resources.IndexStream);
+
+ // write number of reference sequences
+ int32_t numReferences = m_indexFileSummary.size();
+ if ( m_isBigEndian ) SwapEndian_32(numReferences);
+ elementsWritten += fwrite(&numReferences, sizeof(numReferences), 1, Resources.IndexStream);
+
+ if ( elementsWritten != 5 )
+ throw BamException("BamStandardIndex::WriteHeader", "could not write BAI header");
+}
+
+void BamStandardIndex::WriteLinearOffsets(const int& refId, BaiLinearOffsetVector& linearOffsets) {
+
+ // make sure linear offsets are sorted before writing & saving summary
+ SortLinearOffsets(linearOffsets);
+
+ size_t elementsWritten = 0;
+
+ // write number of linear offsets
+ int32_t offsetCount = linearOffsets.size();
+ if ( m_isBigEndian ) SwapEndian_32(offsetCount);
+ elementsWritten += fwrite(&offsetCount, sizeof(offsetCount), 1, Resources.IndexStream);
+
+ // save summary for reference's linear offsets
+ SaveLinearOffsetsSummary(refId, linearOffsets.size());
+
+ // iterate over linear offsets
+ BaiLinearOffsetVector::const_iterator offsetIter = linearOffsets.begin();
+ BaiLinearOffsetVector::const_iterator offsetEnd = linearOffsets.end();
+ for ( ; offsetIter != offsetEnd; ++offsetIter ) {
+
+ // write linear offset
+ uint64_t linearOffset = (*offsetIter);
+ if ( m_isBigEndian ) SwapEndian_64(linearOffset);
+ elementsWritten += fwrite(&linearOffset, sizeof(linearOffset), 1, Resources.IndexStream);
+ }
+
+ if ( elementsWritten != (linearOffsets.size() + 1) )
+ throw BamException("BamStandardIndex::WriteLinearOffsets", "could not write BAI linear offsets");
+}
+
+void BamStandardIndex::WriteReferenceEntry(BaiReferenceEntry& refEntry) {
+ WriteBins(refEntry.ID, refEntry.Bins);
+ WriteLinearOffsets(refEntry.ID, refEntry.LinearOffsets);
+}
projects / bamtools.git / blobdiff