--- /dev/null
+// ***************************************************************************
+// BamIndex.cpp (c) 2009 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 17 August 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides index functionality - both for the default (standardized) BAM
+// index format (.bai) as well as a BamTools-specific (nonstandard) index
+// format (.bti).
+// ***************************************************************************
+
+#include <cstdio>
+#include <cstdlib>
+#include <algorithm>
+// #include <iostream>
+#include <map>
+#include "BamIndex.h"
+#include "BamReader.h"
+#include "BGZF.h"
+using namespace std;
+using namespace BamTools;
+
+// -------------------------------
+// BamIndex implementation
+
+BamIndex::BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader, bool isBigEndian)
+ : m_BGZF(bgzf)
+ , m_reader(reader)
+ , m_isBigEndian(isBigEndian)
+{
+ if ( m_reader && m_reader->IsOpen() )
+ m_references = m_reader->GetReferenceData();
+}
+
+bool BamIndex::HasAlignments(const int& referenceID) {
+
+ // return false if invalid ID
+ if ( (referenceID < 0) || (referenceID >= (int)m_references.size()) )
+ return false;
+
+ // else return status of reference (has alignments?)
+ else
+ return m_references.at(referenceID).RefHasAlignments;
+}
+
+// #########################################################################################
+// #########################################################################################
+
+// -------------------------------
+// BamDefaultIndex structs & typedefs
+
+namespace BamTools {
+
+// --------------------------------------------------
+// BamDefaultIndex data structures & typedefs
+struct Chunk {
+
+ // data members
+ uint64_t Start;
+ uint64_t Stop;
+
+ // constructor
+ Chunk(const uint64_t& start = 0,
+ const uint64_t& stop = 0)
+ : Start(start)
+ , Stop(stop)
+ { }
+};
+
+bool ChunkLessThan(const Chunk& lhs, const Chunk& rhs) {
+ return lhs.Start < rhs.Start;
+}
+
+typedef vector<Chunk> ChunkVector;
+typedef map<uint32_t, ChunkVector> BamBinMap;
+typedef vector<uint64_t> LinearOffsetVector;
+
+struct ReferenceIndex {
+
+ // data members
+ BamBinMap Bins;
+ LinearOffsetVector Offsets;
+
+ // constructor
+ ReferenceIndex(const BamBinMap& binMap = BamBinMap(),
+ const LinearOffsetVector& offsets = LinearOffsetVector())
+ : Bins(binMap)
+ , Offsets(offsets)
+ { }
+};
+
+typedef vector<ReferenceIndex> BamDefaultIndexData;
+
+} // namespace BamTools
+
+// -------------------------------
+// BamDefaultIndex implementation
+
+struct BamDefaultIndex::BamDefaultIndexPrivate {
+
+ // -------------------------
+ // data members
+
+ BamDefaultIndexData m_indexData;
+ BamDefaultIndex* m_parent;
+
+ // -------------------------
+ // ctor & dtor
+
+ BamDefaultIndexPrivate(BamDefaultIndex* parent) : m_parent(parent) { }
+ ~BamDefaultIndexPrivate(void) { }
+
+ // -------------------------
+ // internal methods
+
+ // calculate bins that overlap region
+ int BinsFromRegion(const BamTools::BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[BamTools::MAX_BIN]);
+ // saves BAM bin entry for index
+ void InsertBinEntry(BamBinMap& binMap, const uint32_t& saveBin, const uint64_t& saveOffset, const uint64_t& lastOffset);
+ // saves linear offset entry for index
+ void InsertLinearOffset(LinearOffsetVector& offsets, const BamAlignment& bAlignment, const uint64_t& lastOffset);
+ // simplifies index by merging 'chunks'
+ void MergeChunks(void);
+
+};
+
+BamDefaultIndex::BamDefaultIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian)
+ : BamIndex(bgzf, reader, isBigEndian)
+{
+ d = new BamDefaultIndexPrivate(this);
+}
+
+BamDefaultIndex::~BamDefaultIndex(void) {
+ d->m_indexData.clear();
+ delete d;
+ d = 0;
+}
+
+// calculate bins that overlap region
+int BamDefaultIndex::BamDefaultIndexPrivate::BinsFromRegion(const BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[MAX_BIN]) {
+
+ // get region boundaries
+ uint32_t begin = (unsigned int)region.LeftPosition;
+ uint32_t end;
+
+ // if right bound specified AND left&right bounds are on same reference
+ // OK to use right bound position
+ if ( isRightBoundSpecified && ( region.LeftRefID == region.RightRefID ) )
+ end = (unsigned int)region.RightPosition;
+
+ // otherwise, use end of left bound reference as cutoff
+ else
+ end = (unsigned int)m_parent->m_references.at(region.LeftRefID).RefLength - 1;
+
+ // initialize list, bin '0' always a valid bin
+ int i = 0;
+ bins[i++] = 0;
+
+ // get rest of bins that contain this region
+ unsigned int k;
+ for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { bins[i++] = k; }
+ for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { bins[i++] = k; }
+ for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { bins[i++] = k; }
+ for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { bins[i++] = k; }
+ for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { bins[i++] = k; }
+
+ // return number of bins stored
+ return i;
+}
+
+bool BamDefaultIndex::Build(void) {
+
+ // be sure reader & BGZF file are valid & open for reading
+ if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen )
+ return false;
+
+ // move file pointer to beginning of alignments
+ m_reader->Rewind();
+
+ // get reference count, reserve index space
+ int numReferences = (int)m_references.size();
+ for ( int i = 0; i < numReferences; ++i ) {
+ d->m_indexData.push_back(ReferenceIndex());
+ }
+
+ // sets default constant for bin, ID, offset, coordinate variables
+ const uint32_t defaultValue = 0xffffffffu;
+
+ // bin data
+ uint32_t saveBin(defaultValue);
+ uint32_t lastBin(defaultValue);
+
+ // reference ID data
+ int32_t saveRefID(defaultValue);
+ int32_t lastRefID(defaultValue);
+
+ // offset data
+ uint64_t saveOffset = m_BGZF->Tell();
+ uint64_t lastOffset = saveOffset;
+
+ // coordinate data
+ int32_t lastCoordinate = defaultValue;
+
+ BamAlignment bAlignment;
+ while ( m_reader->GetNextAlignmentCore(bAlignment) ) {
+
+ // change of chromosome, save ID, reset bin
+ if ( lastRefID != bAlignment.RefID ) {
+ lastRefID = bAlignment.RefID;
+ lastBin = defaultValue;
+ }
+
+ // if lastCoordinate greater than BAM position - file not sorted properly
+ else if ( lastCoordinate > bAlignment.Position ) {
+ printf("BAM file not properly sorted:\n");
+ printf("Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
+ exit(1);
+ }
+
+ // if valid reference && BAM bin spans some minimum cutoff (smaller bin ids span larger regions)
+ if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) {
+
+ // save linear offset entry (matched to BAM entry refID)
+ ReferenceIndex& refIndex = d->m_indexData.at(bAlignment.RefID);
+ LinearOffsetVector& offsets = refIndex.Offsets;
+ d->InsertLinearOffset(offsets, bAlignment, lastOffset);
+ }
+
+ // if current BamAlignment bin != lastBin, "then possibly write the binning index"
+ if ( bAlignment.Bin != lastBin ) {
+
+ // if not first time through
+ if ( saveBin != defaultValue ) {
+
+ // save Bam bin entry
+ ReferenceIndex& refIndex = d->m_indexData.at(saveRefID);
+ BamBinMap& binMap = refIndex.Bins;
+ d->InsertBinEntry(binMap, saveBin, saveOffset, lastOffset);
+ }
+
+ // update saveOffset
+ saveOffset = lastOffset;
+
+ // update bin values
+ saveBin = bAlignment.Bin;
+ lastBin = bAlignment.Bin;
+
+ // update saveRefID
+ saveRefID = bAlignment.RefID;
+
+ // if invalid RefID, break out (why?)
+ if ( saveRefID < 0 ) { break; }
+ }
+
+ // make sure that current file pointer is beyond lastOffset
+ if ( m_BGZF->Tell() <= (int64_t)lastOffset ) {
+ printf("Error in BGZF offsets.\n");
+ exit(1);
+ }
+
+ // update lastOffset
+ lastOffset = m_BGZF->Tell();
+
+ // update lastCoordinate
+ lastCoordinate = bAlignment.Position;
+ }
+
+ // save any leftover BAM data (as long as refID is valid)
+ if ( saveRefID >= 0 ) {
+ // save Bam bin entry
+ ReferenceIndex& refIndex = d->m_indexData.at(saveRefID);
+ BamBinMap& binMap = refIndex.Bins;
+ d->InsertBinEntry(binMap, saveBin, saveOffset, lastOffset);
+ }
+
+ // simplify index by merging chunks
+ d->MergeChunks();
+
+ // iterate through references in index
+ // store whether reference has data &
+ // sort offsets in linear offset vector
+ BamDefaultIndexData::iterator indexIter = d->m_indexData.begin();
+ BamDefaultIndexData::iterator indexEnd = d->m_indexData.end();
+ for ( int i = 0; indexIter != indexEnd; ++indexIter, ++i ) {
+
+ // get reference index data
+ ReferenceIndex& refIndex = (*indexIter);
+ BamBinMap& binMap = refIndex.Bins;
+ LinearOffsetVector& offsets = refIndex.Offsets;
+
+ // store whether reference has alignments or no
+ m_references[i].RefHasAlignments = ( binMap.size() > 0 );
+
+ // sort linear offsets
+ sort(offsets.begin(), offsets.end());
+ }
+
+ // rewind file pointer to beginning of alignments, return success/fail
+ return m_reader->Rewind();
+}
+
+bool BamDefaultIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector<int64_t>& offsets) {
+
+ // calculate which bins overlap this region
+ uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2);
+ int numBins = d->BinsFromRegion(region, isRightBoundSpecified, bins);
+
+ // get bins for this reference
+ const ReferenceIndex& refIndex = d->m_indexData.at(region.LeftRefID);
+ const BamBinMap& binMap = refIndex.Bins;
+
+ // get minimum offset to consider
+ const LinearOffsetVector& linearOffsets = refIndex.Offsets;
+ uint64_t minOffset = ( (unsigned int)(region.LeftPosition>>BAM_LIDX_SHIFT) >= linearOffsets.size() ) ? 0 : linearOffsets.at(region.LeftPosition>>BAM_LIDX_SHIFT);
+
+ // store all alignment 'chunk' starts (file offsets) for bins in this region
+ for ( int i = 0; i < numBins; ++i ) {
+
+ const uint16_t binKey = bins[i];
+ map<uint32_t, ChunkVector>::const_iterator binIter = binMap.find(binKey);
+ if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) {
+
+ const ChunkVector& chunks = (*binIter).second;
+ std::vector<Chunk>::const_iterator chunksIter = chunks.begin();
+ std::vector<Chunk>::const_iterator chunksEnd = chunks.end();
+ for ( ; chunksIter != chunksEnd; ++chunksIter) {
+
+ // if valid chunk found, store its file offset
+ const Chunk& chunk = (*chunksIter);
+ if ( chunk.Stop > minOffset )
+ offsets.push_back( chunk.Start );
+ }
+ }
+ }
+
+ // clean up memory
+ free(bins);
+
+ // sort the offsets before returning
+ sort(offsets.begin(), offsets.end());
+
+ // return whether any offsets were found
+ return ( offsets.size() != 0 );
+}
+
+// saves BAM bin entry for index
+void BamDefaultIndex::BamDefaultIndexPrivate::InsertBinEntry(BamBinMap& binMap,
+ const uint32_t& saveBin,
+ const uint64_t& saveOffset,
+ const uint64_t& lastOffset)
+{
+ // look up saveBin
+ BamBinMap::iterator binIter = binMap.find(saveBin);
+
+ // create new chunk
+ Chunk newChunk(saveOffset, lastOffset);
+
+ // if entry doesn't exist
+ if ( binIter == binMap.end() ) {
+ ChunkVector newChunks;
+ newChunks.push_back(newChunk);
+ binMap.insert( pair<uint32_t, ChunkVector>(saveBin, newChunks));
+ }
+
+ // otherwise
+ else {
+ ChunkVector& binChunks = (*binIter).second;
+ binChunks.push_back( newChunk );
+ }
+}
+
+// saves linear offset entry for index
+void BamDefaultIndex::BamDefaultIndexPrivate::InsertLinearOffset(LinearOffsetVector& offsets,
+ const BamAlignment& bAlignment,
+ const uint64_t& lastOffset)
+{
+ // get converted offsets
+ int beginOffset = bAlignment.Position >> BAM_LIDX_SHIFT;
+ int endOffset = (bAlignment.GetEndPosition() - 1) >> 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;
+ }
+}
+
+bool BamDefaultIndex::Load(const string& filename) {
+
+ // open index file, abort on error
+ FILE* indexStream = fopen(filename.c_str(), "rb");
+ if( !indexStream ) {
+ printf("ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
+ return false;
+ }
+
+ // set placeholder to receive input byte count (suppresses compiler warnings)
+ size_t elementsRead = 0;
+
+ // see if index is valid BAM index
+ char magic[4];
+ elementsRead = fread(magic, 1, 4, indexStream);
+ if ( strncmp(magic, "BAI\1", 4) ) {
+ printf("Problem with index file - invalid format.\n");
+ fclose(indexStream);
+ return false;
+ }
+
+ // get number of reference sequences
+ uint32_t numRefSeqs;
+ elementsRead = fread(&numRefSeqs, 4, 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_32(numRefSeqs); }
+
+ // intialize space for BamDefaultIndexData data structure
+ d->m_indexData.reserve(numRefSeqs);
+
+ // iterate over reference sequences
+ for ( unsigned int i = 0; i < numRefSeqs; ++i ) {
+
+ // get number of bins for this reference sequence
+ int32_t numBins;
+ elementsRead = fread(&numBins, 4, 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_32(numBins); }
+
+ if ( numBins > 0 ) {
+ RefData& refEntry = m_references[i];
+ refEntry.RefHasAlignments = true;
+ }
+
+ // intialize BinVector
+ BamBinMap binMap;
+
+ // iterate over bins for that reference sequence
+ for ( int j = 0; j < numBins; ++j ) {
+
+ // get binID
+ uint32_t binID;
+ elementsRead = fread(&binID, 4, 1, indexStream);
+
+ // get number of regionChunks in this bin
+ uint32_t numChunks;
+ elementsRead = fread(&numChunks, 4, 1, indexStream);
+
+ if ( m_isBigEndian ) {
+ SwapEndian_32(binID);
+ SwapEndian_32(numChunks);
+ }
+
+ // intialize ChunkVector
+ ChunkVector regionChunks;
+ regionChunks.reserve(numChunks);
+
+ // iterate over regionChunks in this bin
+ for ( unsigned int k = 0; k < numChunks; ++k ) {
+
+ // get chunk boundaries (left, right)
+ uint64_t left;
+ uint64_t right;
+ elementsRead = fread(&left, 8, 1, indexStream);
+ elementsRead = fread(&right, 8, 1, indexStream);
+
+ if ( m_isBigEndian ) {
+ SwapEndian_64(left);
+ SwapEndian_64(right);
+ }
+
+ // save ChunkPair
+ regionChunks.push_back( Chunk(left, right) );
+ }
+
+ // sort chunks for this bin
+ sort( regionChunks.begin(), regionChunks.end(), ChunkLessThan );
+
+ // save binID, chunkVector for this bin
+ binMap.insert( pair<uint32_t, ChunkVector>(binID, regionChunks) );
+ }
+
+ // load linear index for this reference sequence
+
+ // get number of linear offsets
+ int32_t numLinearOffsets;
+ elementsRead = fread(&numLinearOffsets, 4, 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_32(numLinearOffsets); }
+
+ // intialize LinearOffsetVector
+ LinearOffsetVector offsets;
+ offsets.reserve(numLinearOffsets);
+
+ // iterate over linear offsets for this reference sequeence
+ uint64_t linearOffset;
+ for ( int j = 0; j < numLinearOffsets; ++j ) {
+ // read a linear offset & store
+ elementsRead = fread(&linearOffset, 8, 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_64(linearOffset); }
+ offsets.push_back(linearOffset);
+ }
+
+ // sort linear offsets
+ sort( offsets.begin(), offsets.end() );
+
+ // store index data for that reference sequence
+ d->m_indexData.push_back( ReferenceIndex(binMap, offsets) );
+ }
+
+ // close index file (.bai) and return
+ fclose(indexStream);
+ return true;
+}
+
+// merges 'alignment chunks' in BAM bin (used for index building)
+void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) {
+
+ // iterate over reference enties
+ BamDefaultIndexData::iterator indexIter = m_indexData.begin();
+ BamDefaultIndexData::iterator indexEnd = m_indexData.end();
+ for ( ; indexIter != indexEnd; ++indexIter ) {
+
+ // get BAM bin map for this reference
+ ReferenceIndex& refIndex = (*indexIter);
+ BamBinMap& bamBinMap = refIndex.Bins;
+
+ // iterate over BAM bins
+ BamBinMap::iterator binIter = bamBinMap.begin();
+ BamBinMap::iterator binEnd = bamBinMap.end();
+ for ( ; binIter != binEnd; ++binIter ) {
+
+ // get chunk vector for this bin
+ ChunkVector& binChunks = (*binIter).second;
+ if ( binChunks.size() == 0 ) { continue; }
+
+ ChunkVector mergedChunks;
+ mergedChunks.push_back( binChunks[0] );
+
+ // iterate over chunks
+ int i = 0;
+ ChunkVector::iterator chunkIter = binChunks.begin();
+ ChunkVector::iterator chunkEnd = binChunks.end();
+ for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) {
+
+ // get 'currentChunk' based on numeric index
+ Chunk& currentChunk = mergedChunks[i];
+
+ // get iteratorChunk based on vector iterator
+ Chunk& iteratorChunk = (*chunkIter);
+
+ // if currentChunk.Stop(shifted) == iterator Chunk.Start(shifted)
+ if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) {
+
+ // set currentChunk.Stop to iteratorChunk.Stop
+ currentChunk.Stop = iteratorChunk.Stop;
+ }
+
+ // otherwise
+ else {
+ // set currentChunk + 1 to iteratorChunk
+ mergedChunks.push_back(iteratorChunk);
+ ++i;
+ }
+ }
+
+ // saved merged chunk vector
+ (*binIter).second = mergedChunks;
+ }
+ }
+}
+
+// writes in-memory index data out to file
+// N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
+bool BamDefaultIndex::Write(const std::string& bamFilename) {
+
+ string indexFilename = bamFilename + ".bai";
+ FILE* indexStream = fopen(indexFilename.c_str(), "wb");
+ if ( indexStream == 0 ) {
+ printf("ERROR: Could not open file to save index.\n");
+ return false;
+ }
+
+ // write BAM index header
+ fwrite("BAI\1", 1, 4, indexStream);
+
+ // write number of reference sequences
+ int32_t numReferenceSeqs = d->m_indexData.size();
+ if ( m_isBigEndian ) { SwapEndian_32(numReferenceSeqs); }
+ fwrite(&numReferenceSeqs, 4, 1, indexStream);
+
+ // iterate over reference sequences
+ BamDefaultIndexData::const_iterator indexIter = d->m_indexData.begin();
+ BamDefaultIndexData::const_iterator indexEnd = d->m_indexData.end();
+ for ( ; indexIter != indexEnd; ++ indexIter ) {
+
+ // get reference index data
+ const ReferenceIndex& refIndex = (*indexIter);
+ const BamBinMap& binMap = refIndex.Bins;
+ const LinearOffsetVector& offsets = refIndex.Offsets;
+
+ // write number of bins
+ int32_t binCount = binMap.size();
+ if ( m_isBigEndian ) { SwapEndian_32(binCount); }
+ fwrite(&binCount, 4, 1, indexStream);
+
+ // iterate over bins
+ BamBinMap::const_iterator binIter = binMap.begin();
+ BamBinMap::const_iterator binEnd = binMap.end();
+ for ( ; binIter != binEnd; ++binIter ) {
+
+ // get bin data (key and chunk vector)
+ uint32_t binKey = (*binIter).first;
+ const ChunkVector& binChunks = (*binIter).second;
+
+ // save BAM bin key
+ if ( m_isBigEndian ) { SwapEndian_32(binKey); }
+ fwrite(&binKey, 4, 1, indexStream);
+
+ // save chunk count
+ int32_t chunkCount = binChunks.size();
+ if ( m_isBigEndian ) { SwapEndian_32(chunkCount); }
+ fwrite(&chunkCount, 4, 1, indexStream);
+
+ // iterate over chunks
+ ChunkVector::const_iterator chunkIter = binChunks.begin();
+ ChunkVector::const_iterator chunkEnd = binChunks.end();
+ for ( ; chunkIter != chunkEnd; ++chunkIter ) {
+
+ // get current chunk data
+ const Chunk& chunk = (*chunkIter);
+ uint64_t start = chunk.Start;
+ uint64_t stop = chunk.Stop;
+
+ if ( m_isBigEndian ) {
+ SwapEndian_64(start);
+ SwapEndian_64(stop);
+ }
+
+ // save chunk offsets
+ fwrite(&start, 8, 1, indexStream);
+ fwrite(&stop, 8, 1, indexStream);
+ }
+ }
+
+ // write linear offsets size
+ int32_t offsetSize = offsets.size();
+ if ( m_isBigEndian ) { SwapEndian_32(offsetSize); }
+ fwrite(&offsetSize, 4, 1, indexStream);
+
+ // iterate over linear offsets
+ LinearOffsetVector::const_iterator offsetIter = offsets.begin();
+ LinearOffsetVector::const_iterator offsetEnd = offsets.end();
+ for ( ; offsetIter != offsetEnd; ++offsetIter ) {
+
+ // write linear offset value
+ uint64_t linearOffset = (*offsetIter);
+ if ( m_isBigEndian ) { SwapEndian_64(linearOffset); }
+ fwrite(&linearOffset, 8, 1, indexStream);
+ }
+ }
+
+ // flush buffer, close file, and return success
+ fflush(indexStream);
+ fclose(indexStream);
+ return true;
+}
+
+// #########################################################################################
+// #########################################################################################
+
+// -------------------------------------
+// BamToolsIndex implementation
+
+namespace BamTools {
+
+struct BamToolsIndexEntry {
+
+ // data members
+ int64_t Offset;
+ int RefID;
+ int Position;
+
+ // ctor
+ BamToolsIndexEntry(const uint64_t& offset = 0,
+ const int& id = -1,
+ const int& position = -1)
+ : Offset(offset)
+ , RefID(id)
+ , Position(position)
+ { }
+};
+
+typedef vector<BamToolsIndexEntry> BamToolsIndexData;
+
+} // namespace BamTools
+
+struct BamToolsIndex::BamToolsIndexPrivate {
+
+ // -------------------------
+ // data members
+ BamToolsIndexData m_indexData;
+ BamToolsIndex* m_parent;
+ int32_t m_blockSize;
+
+ // -------------------------
+ // ctor & dtor
+
+ BamToolsIndexPrivate(BamToolsIndex* parent)
+ : m_parent(parent)
+ , m_blockSize(1000)
+ { }
+
+ ~BamToolsIndexPrivate(void) { }
+
+ // -------------------------
+ // internal methods
+};
+
+BamToolsIndex::BamToolsIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian)
+ : BamIndex(bgzf, reader, isBigEndian)
+{
+ d = new BamToolsIndexPrivate(this);
+}
+
+BamToolsIndex::~BamToolsIndex(void) {
+ delete d;
+ d = 0;
+}
+
+bool BamToolsIndex::Build(void) {
+
+ // be sure reader & BGZF file are valid & open for reading
+ if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen )
+ return false;
+
+ // move file pointer to beginning of alignments
+ m_reader->Rewind();
+
+ // plow through alignments, store block offsets
+ int32_t currentBlockCount = 0;
+ int64_t blockStartOffset = m_BGZF->Tell();
+ int blockStartId = -1;
+ int blockStartPosition = -1;
+ BamAlignment al;
+ while ( m_reader->GetNextAlignmentCore(al) ) {
+
+ // set reference flag
+ m_references[al.RefID].RefHasAlignments = true;
+
+ // if beginning of block, save first alignment's refID & position
+ if ( currentBlockCount == 0 ) {
+ blockStartId = al.RefID;
+ blockStartPosition = al.Position;
+ }
+
+ // increment block counter
+ ++currentBlockCount;
+
+ // if block is full, get offset for next block, reset currentBlockCount
+ if ( currentBlockCount == d->m_blockSize ) {
+
+ d->m_indexData.push_back( BamToolsIndexEntry(blockStartOffset, blockStartId, blockStartPosition) );
+ blockStartOffset = m_BGZF->Tell();
+ currentBlockCount = 0;
+ }
+ }
+
+ return m_reader->Rewind();
+}
+
+// N.B. - ignores isRightBoundSpecified
+bool BamToolsIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector<int64_t>& offsets) {
+
+ // return false if no index data present
+ if ( d->m_indexData.empty() ) return false;
+
+ // clear any prior data
+ offsets.clear();
+
+ // calculate nearest index to jump to
+ int64_t previousOffset = -1;
+ BamToolsIndexData::const_iterator indexIter = d->m_indexData.begin();
+ BamToolsIndexData::const_iterator indexEnd = d->m_indexData.end();
+ for ( ; indexIter != indexEnd; ++indexIter ) {
+
+ const BamToolsIndexEntry& entry = (*indexIter);
+
+ // check if we are 'past' beginning of desired region
+ // if so, we will break out & use previously stored offset
+ if ( entry.RefID > region.LeftRefID ) break;
+ if ( (entry.RefID == region.LeftRefID) && (entry.Position > region.LeftPosition) ) break;
+
+ // not past desired region, so store current entry offset in previousOffset
+ previousOffset = entry.Offset;
+ }
+
+ // no index was found
+ if ( previousOffset == -1 )
+ return false;
+
+ // store offset & return success
+ offsets.push_back(previousOffset);
+ return true;
+}
+
+bool BamToolsIndex::Load(const string& filename) {
+
+ // open index file, abort on error
+ FILE* indexStream = fopen(filename.c_str(), "rb");
+ if( !indexStream ) {
+ printf("ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
+ return false;
+ }
+
+ // set placeholder to receive input byte count (suppresses compiler warnings)
+ size_t elementsRead = 0;
+
+ // see if index is valid BAM index
+ char magic[4];
+ elementsRead = fread(magic, 1, 4, indexStream);
+ if ( strncmp(magic, "BTI\1", 4) ) {
+ printf("Problem with index file - invalid format.\n");
+ fclose(indexStream);
+ return false;
+ }
+
+ // read in block size
+ elementsRead = fread(&d->m_blockSize, sizeof(d->m_blockSize), 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_32(d->m_blockSize); }
+
+ // read in number of offsets
+ uint32_t numOffsets;
+ elementsRead = fread(&numOffsets, sizeof(numOffsets), 1, indexStream);
+ if ( m_isBigEndian ) { SwapEndian_32(numOffsets); }
+
+ // reserve space for index data
+ d->m_indexData.reserve(numOffsets);
+
+ // iterate over index entries
+ for ( unsigned int i = 0; i < numOffsets; ++i ) {
+
+ uint64_t offset;
+ int id;
+ int position;
+
+ // read in data
+ elementsRead = fread(&offset, sizeof(offset), 1, indexStream);
+ elementsRead = fread(&id, sizeof(id), 1, indexStream);
+ elementsRead = fread(&position, sizeof(position), 1, indexStream);
+
+ // swap endian-ness if necessary
+ if ( m_isBigEndian ) {
+ SwapEndian_64(offset);
+ SwapEndian_32(id);
+ SwapEndian_32(position);
+ }
+
+ // save reference index entry
+ d->m_indexData.push_back( BamToolsIndexEntry(offset, id, position) );
+
+ // set reference flag
+ m_references[id].RefHasAlignments = true; // what about sparse references? wont be able to set flag?
+ }
+
+ // close index file and return
+ fclose(indexStream);
+ return true;
+}
+
+// writes in-memory index data out to file
+// N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
+bool BamToolsIndex::Write(const std::string& bamFilename) {
+
+ string indexFilename = bamFilename + ".bti";
+ FILE* indexStream = fopen(indexFilename.c_str(), "wb");
+ if ( indexStream == 0 ) {
+ printf("ERROR: Could not open file to save index.\n");
+ return false;
+ }
+
+ // write BAM index header
+ fwrite("BTI\1", 1, 4, indexStream);
+
+ // write block size
+ int32_t blockSize = d->m_blockSize;
+ if ( m_isBigEndian ) { SwapEndian_32(blockSize); }
+ fwrite(&blockSize, sizeof(blockSize), 1, indexStream);
+
+ // write number of offset entries
+ uint32_t numOffsets = d->m_indexData.size();
+ if ( m_isBigEndian ) { SwapEndian_32(numOffsets); }
+ fwrite(&numOffsets, sizeof(numOffsets), 1, indexStream);
+
+ // iterate over offset entries
+ BamToolsIndexData::const_iterator indexIter = d->m_indexData.begin();
+ BamToolsIndexData::const_iterator indexEnd = d->m_indexData.end();
+ for ( ; indexIter != indexEnd; ++ indexIter ) {
+
+ // get reference index data
+ const BamToolsIndexEntry& entry = (*indexIter);
+
+ // copy entry data
+ uint64_t offset = entry.Offset;
+ int id = entry.RefID;
+ int position = entry.Position;
+
+ // swap endian-ness if necessary
+ if ( m_isBigEndian ) {
+ SwapEndian_64(offset);
+ SwapEndian_32(id);
+ SwapEndian_32(position);
+ }
+
+ // write the reference index entry
+ fwrite(&offset, sizeof(offset), 1, indexStream);
+ fwrite(&id, sizeof(id), 1, indexStream);
+ fwrite(&position, sizeof(position), 1, indexStream);
+ }
+
+ // flush file buffer, close file, and return success
+ fflush(indexStream);
+ fclose(indexStream);
+ return true;
+}
projects / bamtools.git / blobdiff