X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamIndex.cpp;h=e72db5ff35c00c481347d6d5277b82d324e71f59;hb=c5363861478f495b41a2ad99028326f85feeb905;hp=5f636d1282567e990e78f4edae019fcac2dda72e;hpb=1ee9b6b3d98a4bfd5a60c583bc7847c545a60e32;p=bamtools.git diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp index 5f636d1..e72db5f 100644 --- a/src/api/BamIndex.cpp +++ b/src/api/BamIndex.cpp @@ -3,7 +3,7 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 17 August 2010 (DB) +// Last modified: 21 October 2010 (DB) // --------------------------------------------------------------------------- // Provides index functionality - both for the default (standardized) BAM // index format (.bai) as well as a BamTools-specific (nonstandard) index @@ -13,7 +13,7 @@ #include #include #include -// #include +#include #include #include "BamIndex.h" #include "BamReader.h" @@ -24,36 +24,162 @@ using namespace BamTools; // ------------------------------- // BamIndex implementation -BamIndex::BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader, bool isBigEndian) +// ctor +BamIndex::BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader) : m_BGZF(bgzf) , m_reader(reader) - , m_isBigEndian(isBigEndian) + , m_cacheMode(BamIndex::LimitedIndexCaching) + , m_indexStream(0) { 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()) ) +// dtor +BamIndex::~BamIndex(void) { + if ( IsOpen() ) + fclose(m_indexStream); +} + +// return true if FILE* is open +bool BamIndex::IsOpen(void) const { + return ( m_indexStream != 0 ); +} + +// loads existing data from file into memory +bool BamIndex::Load(const string& filename) { + + // open index file, abort on error + if ( !OpenIndexFile(filename, "rb") ) { + fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str()); return false; - - // else return status of reference (has alignments?) - else - return m_references.at(referenceID).RefHasAlignments; + } + + // check magic number + if ( !LoadHeader() ) { + fclose(m_indexStream); + return false; + } + + // load reference data (but only keep in memory if full caching requested) + bool saveInitialLoad = ( m_cacheMode == BamIndex::FullIndexCaching ); + if ( !LoadAllReferences(saveInitialLoad) ) { + fclose(m_indexStream); + return false; + } + + // update index cache based on selected mode + UpdateCache(); + + // return success + return true; +} + +// opens index file for reading/writing, return true if opened OK +bool BamIndex::OpenIndexFile(const string& filename, const string& mode) { + m_indexStream = fopen(filename.c_str(), mode.c_str()); + return ( m_indexStream != 0 ); +} + +// rewind index file to beginning of index data, return true if rewound OK +bool BamIndex::Rewind(void) { + return ( fseek64(m_indexStream, DataBeginOffset(), SEEK_SET) == 0 ); +} + +// change the index caching behavior +void BamIndex::SetCacheMode(const BamIndexCacheMode mode) { + if ( mode != m_cacheMode ) { + m_cacheMode = mode; + UpdateCache(); + } +} + +// updates in-memory cache of index data, depending on current cache mode +void BamIndex::UpdateCache(void) { + + // skip if file not open + if ( !IsOpen() ) return; + + // reflect requested cache mode behavior + switch ( m_cacheMode ) { + + case (BamIndex::FullIndexCaching) : + Rewind(); + LoadAllReferences(true); + break; + + case (BamIndex::LimitedIndexCaching) : + if ( HasFullDataCache() ) + KeepOnlyFirstReferenceOffsets(); + else { + ClearAllData(); + SkipToFirstReference(); + LoadFirstReference(true); + } + break; + case(BamIndex::NoIndexCaching) : + ClearAllData(); + break; + default : + // unreachable + ; + } +} + +// writes in-memory index data out to file +bool BamIndex::Write(const string& bamFilename) { + + // open index file for writing + string indexFilename = bamFilename + Extension(); + if ( !OpenIndexFile(indexFilename, "wb") ) { + fprintf(stderr, "ERROR: Could not open file to save index.\n"); + return false; + } + + // write index header data + if ( !WriteHeader() ) { + fprintf(stderr, "ERROR: There was a problem writing index metadata to new index file.\n"); + fflush(m_indexStream); + fclose(m_indexStream); + exit(1); + } + + // write main index data + if ( !WriteAllReferences() ) { + fprintf(stderr, "ERROR: There was a problem writing index data to new index file.\n"); + fflush(m_indexStream); + fclose(m_indexStream); + exit(1); + } + + // flush any remaining output, rewind file, and return success + fflush(m_indexStream); + fclose(m_indexStream); + + // re-open index file for later reading + if ( !OpenIndexFile(indexFilename, "rb") ) { + fprintf(stderr, "ERROR: Could not open newly created index file for reading.\n"); + return false; + } + + // return success/failure of write + return true; } // ######################################################################################### // ######################################################################################### // ------------------------------- -// BamDefaultIndex structs & typedefs +// BamStandardIndex structs & typedefs namespace BamTools { +// BAM index constants +const int MAX_BIN = 37450; // =(8^6-1)/7+1 +const int BAM_LIDX_SHIFT = 14; + // -------------------------------------------------- -// BamDefaultIndex data structures & typedefs +// BamStandardIndex data structures & typedefs struct Chunk { // data members @@ -81,65 +207,164 @@ struct ReferenceIndex { // data members BamBinMap Bins; LinearOffsetVector Offsets; + bool HasAlignments; // constructor - ReferenceIndex(const BamBinMap& binMap = BamBinMap(), - const LinearOffsetVector& offsets = LinearOffsetVector()) + ReferenceIndex(const BamBinMap& binMap = BamBinMap(), + const LinearOffsetVector& offsets = LinearOffsetVector(), + const bool hasAlignments = false) : Bins(binMap) , Offsets(offsets) + , HasAlignments(hasAlignments) { } }; -typedef vector BamDefaultIndexData; +typedef map BamStandardIndexData; } // namespace BamTools // ------------------------------- -// BamDefaultIndex implementation +// BamStandardIndexPrivate implementation -struct BamDefaultIndex::BamDefaultIndexPrivate { +struct BamStandardIndex::BamStandardIndexPrivate { - // ------------------------- - // data members - - BamDefaultIndexData m_indexData; - BamDefaultIndex* m_parent; + // parent object + BamStandardIndex* m_parent; - // ------------------------- - // ctor & dtor + // data members + BamStandardIndexData m_indexData; + off_t m_dataBeginOffset; + bool m_hasFullDataCache; + bool m_isBigEndian; + + // ctor & dtor + BamStandardIndexPrivate(BamStandardIndex* parent); + ~BamStandardIndexPrivate(void); - BamDefaultIndexPrivate(BamDefaultIndex* parent) : m_parent(parent) { } - ~BamDefaultIndexPrivate(void) { } + // parent interface methods + public: + + // creates index data (in-memory) from current reader data + bool Build(void); + // clear all current index offset data in memory + void ClearAllData(void); + // return file position after header metadata + const off_t DataBeginOffset(void) const; + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // return true if all index data is cached + bool HasFullDataCache(void) const; + // attempts to use index to jump to region; returns success/fail + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + // clears index data from all references except the first reference + void KeepOnlyFirstReferenceOffsets(void); + // load index data for all references, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadAllReferences(bool saveData = true); + // load first reference from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadFirstReference(bool saveData = true); + // load header data from index file, return true if loaded OK + bool LoadHeader(void); + // position file pointer to first reference begin, return true if skipped OK + bool SkipToFirstReference(void); + // write header to new index file + bool WriteHeader(void); + // write index data for all references to new index file + bool WriteAllReferences(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); - + private: + + // ----------------------- + // index file operations + + // check index file magic number, return true if OK + bool CheckMagicNumber(void); + // check index file version, return true if OK + bool CheckVersion(void); + // load a single index bin entry from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadBin(ReferenceIndex& refEntry, bool saveData = true); + bool LoadBins(ReferenceIndex& refEntry, bool saveData = true); + // load a single index bin entry from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadChunk(ChunkVector& chunks, bool saveData = true); + bool LoadChunks(ChunkVector& chunks, bool saveData = true); + // load a single index linear offset entry from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadLinearOffsets(ReferenceIndex& refEntry, bool saveData = true); + // load a single reference from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadReference(const int& refId, bool saveData = true); + // loads number of references, return true if loaded OK + bool LoadReferenceCount(int& numReferences); + // position file pointer to desired reference begin, return true if skipped OK + bool SkipToReference(const int& refId); + // write index data for bin to new index file + bool WriteBin(const uint32_t& binId, const ChunkVector& chunks); + // write index data for bins to new index file + bool WriteBins(const BamBinMap& bins); + // write index data for chunk entry to new index file + bool WriteChunk(const Chunk& chunk); + // write index data for chunk entry to new index file + bool WriteChunks(const ChunkVector& chunks); + // write index data for linear offsets entry to new index file + bool WriteLinearOffsets(const LinearOffsetVector& offsets); + // write index data single reference to new index file + bool WriteReference(const ReferenceIndex& refEntry); + + // ----------------------- + // index data operations + + // calculate bins that overlap region + int BinsFromRegion(const BamRegion& region, + const bool isRightBoundSpecified, + uint16_t bins[BamTools::MAX_BIN]); + // clear all index offset data for desired reference + void ClearReferenceOffsets(const int& refId); + // calculates offset(s) for a given region + bool GetOffsets(const BamRegion& region, + const bool isRightBoundSpecified, + vector& offsets, + bool* hasAlignmentsInRegion); + // returns true if index cache has data for desired reference + bool IsDataLoaded(const int& refId) const; + // clears index data from all references except the one specified + void KeepOnlyReferenceOffsets(const int& refId); + // simplifies index by merging 'chunks' + void MergeChunks(void); + // saves BAM bin entry for index + void SaveBinEntry(BamBinMap& binMap, + const uint32_t& saveBin, + const uint64_t& saveOffset, + const uint64_t& lastOffset); + // saves linear offset entry for index + void SaveLinearOffset(LinearOffsetVector& offsets, + const BamAlignment& bAlignment, + const uint64_t& lastOffset); + // initializes index data structure to hold @count references + void SetReferenceCount(const int& count); + }; - -BamDefaultIndex::BamDefaultIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian) - : BamIndex(bgzf, reader, isBigEndian) + +BamStandardIndex::BamStandardIndexPrivate::BamStandardIndexPrivate(BamStandardIndex* parent) + : m_parent(parent) + , m_dataBeginOffset(0) + , m_hasFullDataCache(false) { - d = new BamDefaultIndexPrivate(this); -} + m_isBigEndian = BamTools::SystemIsBigEndian(); +} -BamDefaultIndex::~BamDefaultIndex(void) { - d->m_indexData.clear(); - delete d; - d = 0; +BamStandardIndex::BamStandardIndexPrivate::~BamStandardIndexPrivate(void) { + ClearAllData(); } // calculate bins that overlap region -int BamDefaultIndex::BamDefaultIndexPrivate::BinsFromRegion(const BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[MAX_BIN]) { - +int BamStandardIndex::BamStandardIndexPrivate::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; @@ -169,20 +394,26 @@ int BamDefaultIndex::BamDefaultIndexPrivate::BinsFromRegion(const BamRegion& reg return i; } -bool BamDefaultIndex::Build(void) { +// creates index data (in-memory) from current reader data +bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { + + // localize parent data + if ( m_parent == 0 ) return false; + BamReader* reader = m_parent->m_reader; + BgzfData* mBGZF = m_parent->m_BGZF; // be sure reader & BGZF file are valid & open for reading - if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen ) + if ( reader == 0 || mBGZF == 0 || !mBGZF->IsOpen ) return false; // move file pointer to beginning of alignments - m_reader->Rewind(); + 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()); - } + const int numReferences = (int)m_parent->m_references.size(); + m_indexData.clear(); + m_hasFullDataCache = false; + SetReferenceCount(numReferences); // sets default constant for bin, ID, offset, coordinate variables const uint32_t defaultValue = 0xffffffffu; @@ -196,14 +427,14 @@ bool BamDefaultIndex::Build(void) { int32_t lastRefID(defaultValue); // offset data - uint64_t saveOffset = m_BGZF->Tell(); + uint64_t saveOffset = mBGZF->Tell(); uint64_t lastOffset = saveOffset; // coordinate data int32_t lastCoordinate = defaultValue; BamAlignment bAlignment; - while ( m_reader->GetNextAlignmentCore(bAlignment) ) { + while ( reader->GetNextAlignmentCore(bAlignment) ) { // change of chromosome, save ID, reset bin if ( lastRefID != bAlignment.RefID ) { @@ -214,7 +445,8 @@ bool BamDefaultIndex::Build(void) { // if lastCoordinate greater than BAM position - file not sorted properly else if ( lastCoordinate > bAlignment.Position ) { fprintf(stderr, "BAM file not properly sorted:\n"); - fprintf(stderr, "Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID); + fprintf(stderr, "Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), + lastCoordinate, bAlignment.Position, bAlignment.RefID); exit(1); } @@ -222,9 +454,11 @@ bool BamDefaultIndex::Build(void) { if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) { // save linear offset entry (matched to BAM entry refID) - ReferenceIndex& refIndex = d->m_indexData.at(bAlignment.RefID); + BamStandardIndexData::iterator indexIter = m_indexData.find(bAlignment.RefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; LinearOffsetVector& offsets = refIndex.Offsets; - d->InsertLinearOffset(offsets, bAlignment, lastOffset); + SaveLinearOffset(offsets, bAlignment, lastOffset); } // if current BamAlignment bin != lastBin, "then possibly write the binning index" @@ -234,9 +468,11 @@ bool BamDefaultIndex::Build(void) { if ( saveBin != defaultValue ) { // save Bam bin entry - ReferenceIndex& refIndex = d->m_indexData.at(saveRefID); + BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; BamBinMap& binMap = refIndex.Bins; - d->InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); } // update saveOffset @@ -249,18 +485,18 @@ bool BamDefaultIndex::Build(void) { // update saveRefID saveRefID = bAlignment.RefID; - // if invalid RefID, break out (why?) - if ( saveRefID < 0 ) { break; } + // if invalid RefID, break out + if ( saveRefID < 0 ) break; } // make sure that current file pointer is beyond lastOffset - if ( m_BGZF->Tell() <= (int64_t)lastOffset ) { + if ( mBGZF->Tell() <= (int64_t)lastOffset ) { fprintf(stderr, "Error in BGZF offsets.\n"); exit(1); } // update lastOffset - lastOffset = m_BGZF->Tell(); + lastOffset = mBGZF->Tell(); // update lastCoordinate lastCoordinate = bAlignment.Position; @@ -269,50 +505,115 @@ bool BamDefaultIndex::Build(void) { // 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); + BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; BamBinMap& binMap = refIndex.Bins; - d->InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); } // simplify index by merging chunks - d->MergeChunks(); - + 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(); + BamStandardIndexData::iterator indexIter = m_indexData.begin(); + BamStandardIndexData::iterator indexEnd = m_indexData.end(); for ( int i = 0; indexIter != indexEnd; ++indexIter, ++i ) { // get reference index data - ReferenceIndex& refIndex = (*indexIter); - BamBinMap& binMap = refIndex.Bins; + ReferenceIndex& refIndex = (*indexIter).second; 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(); + return reader->Rewind(); } -bool BamDefaultIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector& offsets) { - +// check index file magic number, return true if OK +bool BamStandardIndex::BamStandardIndexPrivate::CheckMagicNumber(void) { + + // read in magic number + char magic[4]; + size_t elementsRead = fread(magic, sizeof(char), 4, m_parent->m_indexStream); + + // compare to expected value + if ( strncmp(magic, "BAI\1", 4) != 0 ) { + fprintf(stderr, "Problem with index file - invalid format.\n"); + fclose(m_parent->m_indexStream); + return false; + } + + // return success/failure of load + return (elementsRead == 4); +} + +// clear all current index offset data in memory +void BamStandardIndex::BamStandardIndexPrivate::ClearAllData(void) { + BamStandardIndexData::const_iterator indexIter = m_indexData.begin(); + BamStandardIndexData::const_iterator indexEnd = m_indexData.end(); + for ( ; indexIter != indexEnd; ++indexIter ) { + const int& refId = (*indexIter).first; + ClearReferenceOffsets(refId); + } +} + +// clear all index offset data for desired reference +void BamStandardIndex::BamStandardIndexPrivate::ClearReferenceOffsets(const int& refId) { + + // look up refId, skip if not found + BamStandardIndexData::iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end() ) return ; + + // clear reference data + ReferenceIndex& refEntry = (*indexIter).second; + refEntry.Bins.clear(); + refEntry.Offsets.clear(); + + // set flag + m_hasFullDataCache = false; +} + +// return file position after header metadata +const off_t BamStandardIndex::BamStandardIndexPrivate::DataBeginOffset(void) const { + return m_dataBeginOffset; +} + +// calculates offset(s) for a given region +bool BamStandardIndex::BamStandardIndexPrivate::GetOffsets(const BamRegion& region, + const bool isRightBoundSpecified, + vector& offsets, + bool* hasAlignmentsInRegion) +{ + // return false if leftBound refID is not found in index data + if ( m_indexData.find(region.LeftRefID) == m_indexData.end() ) + return false; + + // load index data for region if not already cached + if ( !IsDataLoaded(region.LeftRefID) ) { + bool loadedOk = true; + loadedOk &= SkipToReference(region.LeftRefID); + loadedOk &= LoadReference(region.LeftRefID); + if ( !loadedOk ) return false; + } + // calculate which bins overlap this region uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2); - int numBins = d->BinsFromRegion(region, isRightBoundSpecified, bins); + int numBins = BinsFromRegion(region, isRightBoundSpecified, bins); // get bins for this reference - const ReferenceIndex& refIndex = d->m_indexData.at(region.LeftRefID); + BamStandardIndexData::const_iterator indexIter = m_indexData.find(region.LeftRefID); + if ( indexIter == m_indexData.end() ) return false; // error + const ReferenceIndex& refIndex = (*indexIter).second; 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); + const 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 ) { @@ -321,6 +622,7 @@ bool BamDefaultIndex::GetOffsets(const BamRegion& region, const bool isRightBoun map::const_iterator binIter = binMap.find(binKey); if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) { + // iterate over chunks const ChunkVector& chunks = (*binIter).second; std::vector::const_iterator chunksIter = chunks.begin(); std::vector::const_iterator chunksEnd = chunks.end(); @@ -340,190 +642,332 @@ bool BamDefaultIndex::GetOffsets(const BamRegion& region, const bool isRightBoun // sort the offsets before returning sort(offsets.begin(), offsets.end()); - // return whether any offsets were found - return ( offsets.size() != 0 ); -} + // set flag & return success + *hasAlignmentsInRegion = (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); + // if cache mode set to none, dump the data we just loaded + if (m_parent->m_cacheMode == BamIndex::NoIndexCaching ) + ClearReferenceOffsets(region.LeftRefID); - // create new chunk - Chunk newChunk(saveOffset, lastOffset); + // return succes + return true; +} - // if entry doesn't exist - if ( binIter == binMap.end() ) { - ChunkVector newChunks; - newChunks.push_back(newChunk); - binMap.insert( pair(saveBin, newChunks)); - } +// returns whether reference has alignments or no +bool BamStandardIndex::BamStandardIndexPrivate::HasAlignments(const int& refId) const { + BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end() ) return false; // error + const ReferenceIndex& refEntry = (*indexIter).second; + return refEntry.HasAlignments; +} - // otherwise - else { - ChunkVector& binChunks = (*binIter).second; - binChunks.push_back( newChunk ); - } +// return true if all index data is cached +bool BamStandardIndex::BamStandardIndexPrivate::HasFullDataCache(void) const { + return m_hasFullDataCache; } -// 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; +// returns true if index cache has data for desired reference +bool BamStandardIndex::BamStandardIndexPrivate::IsDataLoaded(const int& refId) const { - // resize vector if necessary - int oldSize = offsets.size(); - int newSize = endOffset + 1; - if ( oldSize < newSize ) - offsets.resize(newSize, 0); + // look up refId, return false if not found + BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end() ) return false; - // store offset - for( int i = beginOffset + 1; i <= endOffset; ++i ) { - if ( offsets[i] == 0 ) - offsets[i] = lastOffset; - } -} + // see if reference has alignments + // if not, it's not a problem to have no offset data + const ReferenceIndex& refEntry = (*indexIter).second; + if ( !refEntry.HasAlignments ) return true; + + // return whether bin map contains data + return ( !refEntry.Bins.empty() ); +} -bool BamDefaultIndex::Load(const string& filename) { +// attempts to use index to jump to region; returns success/fail +bool BamStandardIndex::BamStandardIndexPrivate::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { + + // localize parent data + if ( m_parent == 0 ) return false; + BamReader* reader = m_parent->m_reader; + BgzfData* mBGZF = m_parent->m_BGZF; + RefVector& references = m_parent->m_references; + + // be sure reader & BGZF file are valid & open for reading + if ( reader == 0 || mBGZF == 0 || !mBGZF->IsOpen ) + return false; - // open index file, abort on error - FILE* indexStream = fopen(filename.c_str(), "rb"); - if( !indexStream ) { - fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str()); + // make sure left-bound position is valid + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) 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) ) { - fprintf(stderr, "Problem with index file - invalid format.\n"); - fclose(indexStream); + // calculate offsets for this region + // if failed, print message, set flag, and return failure + vector offsets; + if ( !GetOffsets(region, region.isRightBoundSpecified(), offsets, hasAlignmentsInRegion) ) { + fprintf(stderr, "ERROR: Could not jump: unable to calculate offset(s) for specified region.\n"); + *hasAlignmentsInRegion = false; return false; } + + // iterate through offsets + BamAlignment bAlignment; + bool result = true; + for ( vector::const_iterator o = offsets.begin(); o != offsets.end(); ++o) { + + // attempt seek & load first available alignment + // set flag to true if data exists + result &= mBGZF->Seek(*o); + *hasAlignmentsInRegion = reader->GetNextAlignmentCore(bAlignment); + + // if this alignment corresponds to desired position + // return success of seeking back to the offset before the 'current offset' (to cover overlaps) + if ( ((bAlignment.RefID == region.LeftRefID) && + ((bAlignment.Position + bAlignment.Length) > region.LeftPosition)) || + (bAlignment.RefID > region.LeftRefID) ) + { + if ( o != offsets.begin() ) --o; + return mBGZF->Seek(*o); + } + } + + // if error in jumping, print message & set flag + if ( !result ) { + fprintf(stderr, "ERROR: Could not jump: unable to determine correct offset for specified region.\n"); + *hasAlignmentsInRegion = false; + } + + // return success/failure + return result; +} + +// clears index data from all references except the first +void BamStandardIndex::BamStandardIndexPrivate::KeepOnlyFirstReferenceOffsets(void) { + BamStandardIndexData::const_iterator indexBegin = m_indexData.begin(); + KeepOnlyReferenceOffsets((*indexBegin).first); +} + +// clears index data from all references except the one specified +void BamStandardIndex::BamStandardIndexPrivate::KeepOnlyReferenceOffsets(const int& refId) { + BamStandardIndexData::iterator mapIter = m_indexData.begin(); + BamStandardIndexData::iterator mapEnd = m_indexData.end(); + for ( ; mapIter != mapEnd; ++mapIter ) { + const int entryRefId = (*mapIter).first; + if ( entryRefId != refId ) + ClearReferenceOffsets(entryRefId); + } +} + +bool BamStandardIndex::BamStandardIndexPrivate::LoadAllReferences(bool saveData) { + + // skip if data already loaded + if ( m_hasFullDataCache ) return true; // 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); + uint32_t numReferences; + if ( !LoadReferenceCount((int&)numReferences) ) + return false; - // iterate over reference sequences - for ( unsigned int i = 0; i < numRefSeqs; ++i ) { + // iterate over reference entries + bool loadedOk = true; + for ( int i = 0; i < (int)numReferences; ++i ) + loadedOk &= LoadReference(i, saveData); - // get number of bins for this reference sequence - int32_t numBins; - elementsRead = fread(&numBins, 4, 1, indexStream); - if ( m_isBigEndian ) { SwapEndian_32(numBins); } + // set flag + if ( loadedOk && saveData ) + m_hasFullDataCache = true; - if ( numBins > 0 ) { - RefData& refEntry = m_references[i]; - refEntry.RefHasAlignments = true; - } + // return success/failure of loading references + return loadedOk; +} - // intialize BinVector - BamBinMap binMap; +// load header data from index file, return true if loaded OK +bool BamStandardIndex::BamStandardIndexPrivate::LoadHeader(void) { - // iterate over bins for that reference sequence - for ( int j = 0; j < numBins; ++j ) { + bool loadedOk = CheckMagicNumber(); - // get binID - uint32_t binID; - elementsRead = fread(&binID, 4, 1, indexStream); + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_parent->m_indexStream); - // get number of regionChunks in this bin - uint32_t numChunks; - elementsRead = fread(&numChunks, 4, 1, indexStream); + // return success/failure of load + return loadedOk; +} - 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) ); - } +// load a single index bin entry from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamStandardIndex::BamStandardIndexPrivate::LoadBin(ReferenceIndex& refEntry, bool saveData) { - // sort chunks for this bin - sort( regionChunks.begin(), regionChunks.end(), ChunkLessThan ); + size_t elementsRead = 0; - // save binID, chunkVector for this bin - binMap.insert( pair(binID, regionChunks) ); - } + // get bin ID + uint32_t binId; + elementsRead += fread(&binId, sizeof(binId), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(binId); - // load linear index for this reference sequence + // load alignment chunks for this bin + ChunkVector chunks; + bool chunksOk = LoadChunks(chunks, saveData); - // get number of linear offsets - int32_t numLinearOffsets; - elementsRead = fread(&numLinearOffsets, 4, 1, indexStream); - if ( m_isBigEndian ) { SwapEndian_32(numLinearOffsets); } + // store bin entry + if ( chunksOk && saveData ) + refEntry.Bins.insert(pair(binId, chunks)); - // intialize LinearOffsetVector - LinearOffsetVector offsets; - offsets.reserve(numLinearOffsets); + // return success/failure of load + return ( (elementsRead == 1) && chunksOk ); +} - // 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); - } +bool BamStandardIndex::BamStandardIndexPrivate::LoadBins(ReferenceIndex& refEntry, bool saveData) { - // sort linear offsets - sort( offsets.begin(), offsets.end() ); + size_t elementsRead = 0; + + // get number of bins + int32_t numBins; + elementsRead += fread(&numBins, sizeof(numBins), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numBins); + + // set flag + refEntry.HasAlignments = ( numBins != 0 ); + + // iterate over bins + bool binsOk = true; + for ( int i = 0; i < numBins; ++i ) + binsOk &= LoadBin(refEntry, saveData); + + // return success/failure of load + return ( (elementsRead == 1) && binsOk ); +} + +// load a single index bin entry from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamStandardIndex::BamStandardIndexPrivate::LoadChunk(ChunkVector& chunks, bool saveData) { + + size_t elementsRead = 0; - // store index data for that reference sequence - d->m_indexData.push_back( ReferenceIndex(binMap, offsets) ); + // read in chunk data + uint64_t start; + uint64_t stop; + elementsRead += fread(&start, sizeof(start), 1, m_parent->m_indexStream); + elementsRead += fread(&stop, sizeof(stop), 1, m_parent->m_indexStream); + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_64(start); + SwapEndian_64(stop); } - // close index file (.bai) and return - fclose(indexStream); - return true; + // save data if requested + if ( saveData ) chunks.push_back( Chunk(start, stop) ); + + // return success/failure of load + return ( elementsRead == 2 ); +} + +bool BamStandardIndex::BamStandardIndexPrivate::LoadChunks(ChunkVector& chunks, bool saveData) { + + size_t elementsRead = 0; + + // read in number of chunks + uint32_t numChunks; + elementsRead += fread(&numChunks, sizeof(numChunks), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numChunks); + + // initialize space for chunks if we're storing this data + if ( saveData ) chunks.reserve(numChunks); + + // iterate over chunks + bool chunksOk = true; + for ( int i = 0; i < (int)numChunks; ++i ) + chunksOk &= LoadChunk(chunks, saveData); + + // sort chunk vector + sort( chunks.begin(), chunks.end(), ChunkLessThan ); + + // return success/failure of load + return ( (elementsRead == 1) && chunksOk ); +} + +// load a single index linear offset entry from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamStandardIndex::BamStandardIndexPrivate::LoadLinearOffsets(ReferenceIndex& refEntry, bool saveData) { + + size_t elementsRead = 0; + + // read in number of linear offsets + int32_t numLinearOffsets; + elementsRead += fread(&numLinearOffsets, sizeof(numLinearOffsets), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numLinearOffsets); + + // set up destination vector (if we're saving the data) + LinearOffsetVector linearOffsets; + if ( saveData ) linearOffsets.reserve(numLinearOffsets); + + // iterate over linear offsets + uint64_t linearOffset; + for ( int i = 0; i < numLinearOffsets; ++i ) { + elementsRead += fread(&linearOffset, sizeof(linearOffset), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_64(linearOffset); + if ( saveData ) linearOffsets.push_back(linearOffset); + } + + // sort linear offsets + sort ( linearOffsets.begin(), linearOffsets.end() ); + + // save in reference index entry if desired + if ( saveData ) refEntry.Offsets = linearOffsets; + + // return success/failure of load + return ( elementsRead == (size_t)(numLinearOffsets + 1) ); +} + +bool BamStandardIndex::BamStandardIndexPrivate::LoadFirstReference(bool saveData) { + BamStandardIndexData::const_iterator indexBegin = m_indexData.begin(); + return LoadReference((*indexBegin).first, saveData); +} + +// load a single reference from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamStandardIndex::BamStandardIndexPrivate::LoadReference(const int& refId, bool saveData) { + + // look up refId + BamStandardIndexData::iterator indexIter = m_indexData.find(refId); + + // if reference not previously loaded, create new entry + if ( indexIter == m_indexData.end() ) { + ReferenceIndex newEntry; + newEntry.HasAlignments = false; + m_indexData.insert( pair(refId, newEntry) ); + } + + // load reference data + indexIter = m_indexData.find(refId); + ReferenceIndex& entry = (*indexIter).second; + bool loadedOk = true; + loadedOk &= LoadBins(entry, saveData); + loadedOk &= LoadLinearOffsets(entry, saveData); + return loadedOk; +} + +// loads number of references, return true if loaded OK +bool BamStandardIndex::BamStandardIndexPrivate::LoadReferenceCount(int& numReferences) { + + size_t elementsRead = 0; + + // read reference count + elementsRead += fread(&numReferences, sizeof(numReferences), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + + // return success/failure of load + return ( elementsRead == 1 ); } // merges 'alignment chunks' in BAM bin (used for index building) -void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) { +void BamStandardIndex::BamStandardIndexPrivate::MergeChunks(void) { // iterate over reference enties - BamDefaultIndexData::iterator indexIter = m_indexData.begin(); - BamDefaultIndexData::iterator indexEnd = m_indexData.end(); + BamStandardIndexData::iterator indexIter = m_indexData.begin(); + BamStandardIndexData::iterator indexEnd = m_indexData.end(); for ( ; indexIter != indexEnd; ++indexIter ) { // get BAM bin map for this reference - ReferenceIndex& refIndex = (*indexIter); + ReferenceIndex& refIndex = (*indexIter).second; BamBinMap& bamBinMap = refIndex.Bins; // iterate over BAM bins @@ -533,7 +977,7 @@ void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) { // get chunk vector for this bin ChunkVector& binChunks = (*binIter).second; - if ( binChunks.size() == 0 ) { continue; } + if ( binChunks.size() == 0 ) continue; ChunkVector mergedChunks; mergedChunks.push_back( binChunks[0] ); @@ -550,12 +994,9 @@ void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) { // 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 + // if chunk ends where (iterator) chunk starts, then merge + if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) currentChunk.Stop = iteratorChunk.Stop; - } // otherwise else { @@ -571,356 +1012,1023 @@ void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) { } } -// 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 ) { - fprintf(stderr, "ERROR: Could not open file to save index.\n"); - return false; - } +// saves BAM bin entry for index +void BamStandardIndex::BamStandardIndexPrivate::SaveBinEntry(BamBinMap& binMap, + const uint32_t& saveBin, + const uint64_t& saveOffset, + const uint64_t& lastOffset) +{ + // look up saveBin + BamBinMap::iterator binIter = binMap.find(saveBin); - // write BAM index header - fwrite("BAI\1", 1, 4, indexStream); + // create new chunk + Chunk newChunk(saveOffset, lastOffset); - // write number of reference sequences - int32_t numReferenceSeqs = d->m_indexData.size(); - if ( m_isBigEndian ) { SwapEndian_32(numReferenceSeqs); } - fwrite(&numReferenceSeqs, 4, 1, indexStream); + // if entry doesn't exist + if ( binIter == binMap.end() ) { + ChunkVector newChunks; + newChunks.push_back(newChunk); + binMap.insert( pair(saveBin, newChunks)); + } - // iterate over reference sequences - BamDefaultIndexData::const_iterator indexIter = d->m_indexData.begin(); - BamDefaultIndexData::const_iterator indexEnd = d->m_indexData.end(); - for ( ; indexIter != indexEnd; ++ indexIter ) { + // otherwise + else { + ChunkVector& binChunks = (*binIter).second; + binChunks.push_back( newChunk ); + } +} - // 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 ) { +// saves linear offset entry for index +void BamStandardIndex::BamStandardIndexPrivate::SaveLinearOffset(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; - // get bin data (key and chunk vector) - uint32_t binKey = (*binIter).first; - const ChunkVector& binChunks = (*binIter).second; + // resize vector if necessary + int oldSize = offsets.size(); + int newSize = endOffset + 1; + if ( oldSize < newSize ) + offsets.resize(newSize, 0); - // save BAM bin key - if ( m_isBigEndian ) { SwapEndian_32(binKey); } - fwrite(&binKey, 4, 1, indexStream); + // store offset + for( int i = beginOffset + 1; i <= endOffset; ++i ) { + if ( offsets[i] == 0 ) + offsets[i] = lastOffset; + } +} - // save chunk count - int32_t chunkCount = binChunks.size(); - if ( m_isBigEndian ) { SwapEndian_32(chunkCount); } - fwrite(&chunkCount, 4, 1, indexStream); +// initializes index data structure to hold @count references +void BamStandardIndex::BamStandardIndexPrivate::SetReferenceCount(const int& count) { + for ( int i = 0; i < count; ++i ) + m_indexData[i].HasAlignments = false; +} - // 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); - } - } +bool BamStandardIndex::BamStandardIndexPrivate::SkipToFirstReference(void) { + BamStandardIndexData::const_iterator indexBegin = m_indexData.begin(); + return SkipToReference( (*indexBegin).first ); +} - // write linear offsets size - int32_t offsetSize = offsets.size(); - if ( m_isBigEndian ) { SwapEndian_32(offsetSize); } - fwrite(&offsetSize, 4, 1, indexStream); +// position file pointer to desired reference begin, return true if skipped OK +bool BamStandardIndex::BamStandardIndexPrivate::SkipToReference(const int& refId) { - // iterate over linear offsets - LinearOffsetVector::const_iterator offsetIter = offsets.begin(); - LinearOffsetVector::const_iterator offsetEnd = offsets.end(); - for ( ; offsetIter != offsetEnd; ++offsetIter ) { + // attempt rewind + if ( !m_parent->Rewind() ) return false; - // write linear offset value - uint64_t linearOffset = (*offsetIter); - if ( m_isBigEndian ) { SwapEndian_64(linearOffset); } - fwrite(&linearOffset, 8, 1, indexStream); - } + // read in number of references + uint32_t numReferences; + size_t elementsRead = fread(&numReferences, sizeof(numReferences), 1, m_parent->m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(numReferences); + + // iterate over reference entries + bool skippedOk = true; + int currentRefId = 0; + while (currentRefId != refId) { + skippedOk &= LoadReference(currentRefId, false); + ++currentRefId; } - // flush buffer, close file, and return success - fflush(indexStream); - fclose(indexStream); - return true; + // return success + return skippedOk; } + +// write header to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write magic number + elementsWritten += fwrite("BAI\1", sizeof(char), 4, m_parent->m_indexStream); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_parent->m_indexStream); + + // return success/failure of write + return (elementsWritten == 4); +} + +// write index data for all references to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteAllReferences(void) { + + size_t elementsWritten = 0; + + // write number of reference sequences + int32_t numReferenceSeqs = m_indexData.size(); + if ( m_isBigEndian ) SwapEndian_32(numReferenceSeqs); + elementsWritten += fwrite(&numReferenceSeqs, sizeof(numReferenceSeqs), 1, m_parent->m_indexStream); + + // iterate over reference sequences + bool refsOk = true; + BamStandardIndexData::const_iterator indexIter = m_indexData.begin(); + BamStandardIndexData::const_iterator indexEnd = m_indexData.end(); + for ( ; indexIter != indexEnd; ++ indexIter ) + refsOk &= WriteReference( (*indexIter).second ); + + // return success/failure of write + return ( (elementsWritten == 1) && refsOk ); +} + +// write index data for bin to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteBin(const uint32_t& binId, const ChunkVector& chunks) { + + size_t elementsWritten = 0; + + // write BAM bin ID + uint32_t binKey = binId; + if ( m_isBigEndian ) SwapEndian_32(binKey); + elementsWritten += fwrite(&binKey, sizeof(binKey), 1, m_parent->m_indexStream); + + // write chunks + bool chunksOk = WriteChunks(chunks); + + // return success/failure of write + return ( (elementsWritten == 1) && chunksOk ); +} + +// write index data for bins to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteBins(const BamBinMap& bins) { + + size_t elementsWritten = 0; + + // write number of bins + int32_t binCount = bins.size(); + if ( m_isBigEndian ) SwapEndian_32(binCount); + elementsWritten += fwrite(&binCount, sizeof(binCount), 1, m_parent->m_indexStream); + + // iterate over bins + bool binsOk = true; + BamBinMap::const_iterator binIter = bins.begin(); + BamBinMap::const_iterator binEnd = bins.end(); + for ( ; binIter != binEnd; ++binIter ) + binsOk &= WriteBin( (*binIter).first, (*binIter).second ); + + // return success/failure of write + return ( (elementsWritten == 1) && binsOk ); +} + +// write index data for chunk entry to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteChunk(const Chunk& chunk) { + + size_t elementsWritten = 0; + + // 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 + elementsWritten += fwrite(&start, sizeof(start), 1, m_parent->m_indexStream); + elementsWritten += fwrite(&stop, sizeof(stop), 1, m_parent->m_indexStream); + + // return success/failure of write + return ( elementsWritten == 2 ); +} + +// write index data for chunk entry to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteChunks(const ChunkVector& chunks) { + + size_t elementsWritten = 0; + + // write chunks + int32_t chunkCount = chunks.size(); + if ( m_isBigEndian ) SwapEndian_32(chunkCount); + elementsWritten += fwrite(&chunkCount, sizeof(chunkCount), 1, m_parent->m_indexStream); + + // iterate over chunks + bool chunksOk = true; + ChunkVector::const_iterator chunkIter = chunks.begin(); + ChunkVector::const_iterator chunkEnd = chunks.end(); + for ( ; chunkIter != chunkEnd; ++chunkIter ) + chunksOk &= WriteChunk( (*chunkIter) ); + + // return success/failure of write + return ( (elementsWritten == 1) && chunksOk ); +} + +// write index data for linear offsets entry to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteLinearOffsets(const LinearOffsetVector& offsets) { + + size_t elementsWritten = 0; + + // write number of linear offsets + int32_t offsetCount = offsets.size(); + if ( m_isBigEndian ) SwapEndian_32(offsetCount); + elementsWritten += fwrite(&offsetCount, sizeof(offsetCount), 1, m_parent->m_indexStream); + + // iterate over linear offsets + LinearOffsetVector::const_iterator offsetIter = offsets.begin(); + LinearOffsetVector::const_iterator offsetEnd = offsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) { + + // write linear offset + uint64_t linearOffset = (*offsetIter); + if ( m_isBigEndian ) SwapEndian_64(linearOffset); + elementsWritten += fwrite(&linearOffset, sizeof(linearOffset), 1, m_parent->m_indexStream); + } + + // return success/failure of write + return ( elementsWritten == (size_t)(offsetCount + 1) ); +} + +// write index data for a single reference to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteReference(const ReferenceIndex& refEntry) { + bool refOk = true; + refOk &= WriteBins(refEntry.Bins); + refOk &= WriteLinearOffsets(refEntry.Offsets); + return refOk; +} + +// --------------------------------------------------------------- +// BamStandardIndex implementation + +BamStandardIndex::BamStandardIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) +{ + d = new BamStandardIndexPrivate(this); +} + +BamStandardIndex::~BamStandardIndex(void) { + delete d; + d = 0; +} + +// BamIndex interface implementation +bool BamStandardIndex::Build(void) { return d->Build(); } +void BamStandardIndex::ClearAllData(void) { d->ClearAllData(); } +const off_t BamStandardIndex::DataBeginOffset(void) const { return d->DataBeginOffset(); } +bool BamStandardIndex::HasAlignments(const int& referenceID) const { return d->HasAlignments(referenceID); } +bool BamStandardIndex::HasFullDataCache(void) const { return d->HasFullDataCache(); } +bool BamStandardIndex::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { return d->Jump(region, hasAlignmentsInRegion); } +void BamStandardIndex::KeepOnlyFirstReferenceOffsets(void) { d->KeepOnlyFirstReferenceOffsets(); } +bool BamStandardIndex::LoadAllReferences(bool saveData) { return d->LoadAllReferences(saveData); } +bool BamStandardIndex::LoadFirstReference(bool saveData) { return d->LoadFirstReference(saveData); } +bool BamStandardIndex::LoadHeader(void) { return d->LoadHeader(); } +bool BamStandardIndex::SkipToFirstReference(void) { return d->SkipToFirstReference(); } +bool BamStandardIndex::WriteAllReferences(void) { return d->WriteAllReferences(); } +bool BamStandardIndex::WriteHeader(void) { return d->WriteHeader(); } // ######################################################################################### // ######################################################################################### -// ------------------------------------- -// BamToolsIndex implementation +// --------------------------------------------------- +// BamToolsIndex structs & typedefs namespace BamTools { +// individual index offset entry struct BamToolsIndexEntry { // data members - int64_t Offset; - int RefID; - int Position; + int32_t MaxEndPosition; + int64_t StartOffset; + int32_t StartPosition; // ctor - BamToolsIndexEntry(const uint64_t& offset = 0, - const int& id = -1, - const int& position = -1) - : Offset(offset) - , RefID(id) - , Position(position) + BamToolsIndexEntry(const int32_t& maxEndPosition = 0, + const int64_t& startOffset = 0, + const int32_t& startPosition = 0) + : MaxEndPosition(maxEndPosition) + , StartOffset(startOffset) + , StartPosition(startPosition) + { } +}; + +// reference index entry +struct BamToolsReferenceEntry { + + // data members + bool HasAlignments; + vector Offsets; + + // ctor + BamToolsReferenceEntry(void) + : HasAlignments(false) { } }; -typedef vector BamToolsIndexData; +// the actual index data structure +typedef map BamToolsIndexData; } // namespace BamTools +// --------------------------------------------------- +// BamToolsIndexPrivate implementation + struct BamToolsIndex::BamToolsIndexPrivate { + + // keep a list of any supported versions here + // (might be useful later to handle any 'legacy' versions if the format changes) + // listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on + // + // so a change introduced in (hypothetical) BTI_1_2 would be handled from then on by: + // + // if ( indexVersion >= BTI_1_2 ) + // do something new + // else + // do the old thing + enum Version { BTI_1_0 = 1 + , BTI_1_1 + , BTI_1_2 + }; - // ------------------------- + // parent object + BamToolsIndex* m_parent; + // data members - BamToolsIndexData m_indexData; - BamToolsIndex* m_parent; int32_t m_blockSize; + BamToolsIndexData m_indexData; + off_t m_dataBeginOffset; + bool m_hasFullDataCache; + bool m_isBigEndian; + int32_t m_inputVersion; // Version is serialized as int + Version m_outputVersion; - // ------------------------- - // ctor & dtor - - BamToolsIndexPrivate(BamToolsIndex* parent) - : m_parent(parent) - , m_blockSize(1000) - { } + // ctor & dtor + BamToolsIndexPrivate(BamToolsIndex* parent); + ~BamToolsIndexPrivate(void); - ~BamToolsIndexPrivate(void) { } + // parent interface methods + public: + + // creates index data (in-memory) from current reader data + bool Build(void); + // clear all current index offset data in memory + void ClearAllData(void); + // return file position after header metadata + const off_t DataBeginOffset(void) const; + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // return true if all index data is cached + bool HasFullDataCache(void) const; + // attempts to use index to jump to region; returns success/fail + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + // clears index data from all references except the first + void KeepOnlyFirstReferenceOffsets(void); + // load index data for all references, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadAllReferences(bool saveData = true); + // load first reference from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadFirstReference(bool saveData = true); + // load header data from index file, return true if loaded OK + bool LoadHeader(void); + // position file pointer to desired reference begin, return true if skipped OK + bool SkipToFirstReference(void); + // write header to new index file + bool WriteHeader(void); + // write index data for all references to new index file + bool WriteAllReferences(void); - // ------------------------- // internal methods + private: + + // ----------------------- + // index file operations + + // check index file magic number, return true if OK + bool CheckMagicNumber(void); + // check index file version, return true if OK + bool CheckVersion(void); + // return true if FILE* is open + bool IsOpen(void) const; + // load a single index entry from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadIndexEntry(const int& refId, bool saveData = true); + // load a single reference from file, return true if loaded OK + // @saveData - save data in memory if true, just read & discard if false + bool LoadReference(const int& refId, bool saveData = true); + // loads number of references, return true if loaded OK + bool LoadReferenceCount(int& numReferences); + // position file pointer to desired reference begin, return true if skipped OK + bool SkipToReference(const int& refId); + // write current reference index data to new index file + bool WriteReferenceEntry(const BamToolsReferenceEntry& refEntry); + // write current index offset entry to new index file + bool WriteIndexEntry(const BamToolsIndexEntry& entry); + + // ----------------------- + // index data operations + + // clear all index offset data for desired reference + void ClearReferenceOffsets(const int& refId); + // calculate BAM file offset for desired region + // return true if no error (*NOT* equivalent to "has alignments or valid offset") + // check @hasAlignmentsInRegion to determine this status + // @region - target region + // @offset - resulting seek target + // @hasAlignmentsInRegion - sometimes a file just lacks data in region, this flag indicates that status + bool GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion); + // returns true if index cache has data for desired reference + bool IsDataLoaded(const int& refId) const; + // clears index data from all references except the one specified + void KeepOnlyReferenceOffsets(const int& refId); + // saves an index offset entry in memory + void SaveOffsetEntry(const int& refId, const BamToolsIndexEntry& entry); + // pre-allocates size for offset vector + void SetOffsetCount(const int& refId, const int& offsetCount); + // initializes index data structure to hold @count references + void SetReferenceCount(const int& count); }; -BamToolsIndex::BamToolsIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian) - : BamIndex(bgzf, reader, isBigEndian) -{ - d = new BamToolsIndexPrivate(this); -} +// ctor +BamToolsIndex::BamToolsIndexPrivate::BamToolsIndexPrivate(BamToolsIndex* parent) + : m_parent(parent) + , m_blockSize(1000) + , m_dataBeginOffset(0) + , m_hasFullDataCache(false) + , m_inputVersion(0) + , m_outputVersion(BTI_1_2) // latest version - used for writing new index files +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} -BamToolsIndex::~BamToolsIndex(void) { - delete d; - d = 0; +// dtor +BamToolsIndex::BamToolsIndexPrivate::~BamToolsIndexPrivate(void) { + ClearAllData(); } -bool BamToolsIndex::Build(void) { +// creates index data (in-memory) from current reader data +bool BamToolsIndex::BamToolsIndexPrivate::Build(void) { + + // localize parent data + if ( m_parent == 0 ) return false; + BamReader* reader = m_parent->m_reader; + BgzfData* mBGZF = m_parent->m_BGZF; // be sure reader & BGZF file are valid & open for reading - if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen ) + if ( reader == 0 || mBGZF == 0 || !mBGZF->IsOpen ) return false; // move file pointer to beginning of alignments - m_reader->Rewind(); + if ( !reader->Rewind() ) return false; + + // initialize index data structure with space for all references + const int numReferences = (int)m_parent->m_references.size(); + m_indexData.clear(); + m_hasFullDataCache = false; + SetReferenceCount(numReferences); + + // set up counters and markers + int32_t currentBlockCount = 0; + int64_t currentAlignmentOffset = mBGZF->Tell(); + int32_t blockRefId = 0; + int32_t blockMaxEndPosition = 0; + int64_t blockStartOffset = currentAlignmentOffset; + int32_t blockStartPosition = -1; - // plow through alignments, store block offsets - int32_t currentBlockCount = 0; - int64_t blockStartOffset = m_BGZF->Tell(); - int blockStartId = -1; - int blockStartPosition = -1; + // plow through alignments, storing index entries BamAlignment al; - while ( m_reader->GetNextAlignmentCore(al) ) { + while ( reader->GetNextAlignmentCore(al) ) { + + // if block contains data (not the first time through) AND alignment is on a new reference + if ( currentBlockCount > 0 && al.RefID != blockRefId ) { + + // store previous data + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); + + // intialize new block for current alignment's reference + currentBlockCount = 0; + blockMaxEndPosition = al.GetEndPosition(); + blockStartOffset = currentAlignmentOffset; + } - // 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; + blockRefId = al.RefID; blockStartPosition = al.Position; } // increment block counter ++currentBlockCount; + + // check end position + int32_t alignmentEndPosition = al.GetEndPosition(); + if ( alignmentEndPosition > blockMaxEndPosition ) + blockMaxEndPosition = alignmentEndPosition; // 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(); + if ( currentBlockCount == m_blockSize ) { + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); + blockStartOffset = mBGZF->Tell(); currentBlockCount = 0; } + + // not the best name, but for the next iteration, this value will be the offset of the *current* alignment + // necessary because we won't know if this next alignment is on a new reference until we actually read it + currentAlignmentOffset = mBGZF->Tell(); } - return m_reader->Rewind(); + // store final block with data + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); + + // set flag + m_hasFullDataCache = true; + + // return success/failure of rewind + return reader->Rewind(); } -// N.B. - ignores isRightBoundSpecified -bool BamToolsIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector& offsets) { - - // return false if no index data present - if ( d->m_indexData.empty() ) return false; - - // clear any prior data +// check index file magic number, return true if OK +bool BamToolsIndex::BamToolsIndexPrivate::CheckMagicNumber(void) { + + // see if index is valid BAM index + char magic[4]; + size_t elementsRead = fread(magic, 1, 4, m_parent->m_indexStream); + if ( elementsRead != 4 ) return false; + if ( strncmp(magic, "BTI\1", 4) != 0 ) { + fprintf(stderr, "Problem with index file - invalid format.\n"); + return false; + } + + // otherwise ok + return true; +} + +// check index file version, return true if OK +bool BamToolsIndex::BamToolsIndexPrivate::CheckVersion(void) { + + // read version from file + size_t elementsRead = fread(&m_inputVersion, sizeof(m_inputVersion), 1, m_parent->m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(m_inputVersion); + + // if version is negative, or zero + if ( m_inputVersion <= 0 ) { + fprintf(stderr, "Problem with index file - invalid version.\n"); + return false; + } + + // if version is newer than can be supported by this version of bamtools + else if ( m_inputVersion > m_outputVersion ) { + fprintf(stderr, "Problem with index file - attempting to use an outdated version of BamTools with a newer index file.\n"); + fprintf(stderr, "Please update BamTools to a more recent version to support this index file.\n"); + return false; + } + + // ------------------------------------------------------------------ + // check for deprecated, unsupported versions + // (typically whose format did not accomodate a particular bug fix) + + else if ( (Version)m_inputVersion == BTI_1_0 ) { + fprintf(stderr, "\nProblem with index file - this version of the index contains a bug related to accessing data near reference ends.\n"); + fprintf(stderr, "\nPlease run \'bamtools index -bti -in yourData.bam\' to generate an up-to-date BamToolsIndex.\n\n"); + return false; + } + + else if ( (Version)m_inputVersion == BTI_1_1 ) { + fprintf(stderr, "\nProblem with index file - this version of the index contains a bug related to handling empty references.\n"); + fprintf(stderr, "\nPlease run \'bamtools index -bti -in yourData.bam\' to generate an up-to-date BamToolsIndex.\n\n"); + return false; + } + + // otherwise ok + else return true; +} + +// clear all current index offset data in memory +void BamToolsIndex::BamToolsIndexPrivate::ClearAllData(void) { + BamToolsIndexData::const_iterator indexIter = m_indexData.begin(); + BamToolsIndexData::const_iterator indexEnd = m_indexData.end(); + for ( ; indexIter != indexEnd; ++indexIter ) { + const int& refId = (*indexIter).first; + ClearReferenceOffsets(refId); + } +} + +// clear all index offset data for desired reference +void BamToolsIndex::BamToolsIndexPrivate::ClearReferenceOffsets(const int& refId) { + if ( m_indexData.find(refId) == m_indexData.end() ) return; + vector& offsets = m_indexData[refId].Offsets; offsets.clear(); + m_hasFullDataCache = false; +} + +// return file position after header metadata +const off_t BamToolsIndex::BamToolsIndexPrivate::DataBeginOffset(void) const { + return m_dataBeginOffset; +} + +// calculate BAM file offset for desired region +// return true if no error (*NOT* equivalent to "has alignments or valid offset") +// check @hasAlignmentsInRegion to determine this status +// @region - target region +// @offset - resulting seek target +// @hasAlignmentsInRegion - sometimes a file just lacks data in region, this flag indicates that status +// N.B. - ignores isRightBoundSpecified +bool BamToolsIndex::BamToolsIndexPrivate::GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion) { + // return false if leftBound refID is not found in index data + BamToolsIndexData::const_iterator indexIter = m_indexData.find(region.LeftRefID); + if ( indexIter == m_indexData.end()) return false; + + // load index data for region if not already cached + if ( !IsDataLoaded(region.LeftRefID) ) { + bool loadedOk = true; + loadedOk &= SkipToReference(region.LeftRefID); + loadedOk &= LoadReference(region.LeftRefID); + if ( !loadedOk ) return false; + } + + // localize index data for this reference (& sanity check that data actually exists) + indexIter = m_indexData.find(region.LeftRefID); + if ( indexIter == m_indexData.end()) return false; + const vector& referenceOffsets = (*indexIter).second.Offsets; + if ( referenceOffsets.empty() ) return false; + + // ------------------------------------------------------- // 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; + + // save first offset + offset = (*referenceOffsets.begin()).StartOffset; + + // iterate over offsets entries on this reference + vector::const_iterator offsetIter = referenceOffsets.begin(); + vector::const_iterator offsetEnd = referenceOffsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) { + const BamToolsIndexEntry& entry = (*offsetIter); + // break if alignment 'entry' overlaps region + if ( entry.MaxEndPosition >= region.LeftPosition ) break; + offset = (*offsetIter).StartOffset; } - // no index was found - if ( previousOffset == -1 ) - return false; - - // store offset & return success - offsets.push_back(previousOffset); + // set flag based on whether an index entry was found for this region + *hasAlignmentsInRegion = ( offsetIter != offsetEnd ); + + // if cache mode set to none, dump the data we just loaded + if (m_parent->m_cacheMode == BamIndex::NoIndexCaching ) + ClearReferenceOffsets(region.LeftRefID); + + // return success return true; } -bool BamToolsIndex::Load(const string& filename) { +// returns whether reference has alignments or no +bool BamToolsIndex::BamToolsIndexPrivate::HasAlignments(const int& refId) const { + + BamToolsIndexData::const_iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end()) return false; + const BamToolsReferenceEntry& refEntry = (*indexIter).second; + return refEntry.HasAlignments; +} + +// return true if all index data is cached +bool BamToolsIndex::BamToolsIndexPrivate::HasFullDataCache(void) const { + return m_hasFullDataCache; +} + +// returns true if index cache has data for desired reference +bool BamToolsIndex::BamToolsIndexPrivate::IsDataLoaded(const int& refId) const { + + BamToolsIndexData::const_iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end()) return false; + const BamToolsReferenceEntry& refEntry = (*indexIter).second; + + if ( !refEntry.HasAlignments ) return true; // no data period + + // return whether offsets list contains data + return !refEntry.Offsets.empty(); +} + +// attempts to use index to jump to region; returns success/fail +bool BamToolsIndex::BamToolsIndexPrivate::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { - // open index file, abort on error - FILE* indexStream = fopen(filename.c_str(), "rb"); - if( !indexStream ) { - fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str()); + // clear flag + *hasAlignmentsInRegion = false; + + // localize parent data + if ( m_parent == 0 ) return false; + BamReader* reader = m_parent->m_reader; + BgzfData* mBGZF = m_parent->m_BGZF; + RefVector& references = m_parent->m_references; + + // check valid BamReader state + if ( reader == 0 || mBGZF == 0 || !reader->IsOpen() ) { + fprintf(stderr, "ERROR: Could not jump: invalid BamReader state.\n"); 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) ) { - fprintf(stderr, "Problem with index file - invalid format.\n"); - fclose(indexStream); + + // make sure left-bound position is valid + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) + return false; + + // calculate nearest offset to jump to + int64_t offset; + if ( !GetOffset(region, offset, hasAlignmentsInRegion) ) { + fprintf(stderr, "ERROR: Could not jump - unable to calculate offset for specified region.\n"); return false; } + + // return success/failure of seek + return mBGZF->Seek(offset); +} + +// clears index data from all references except the first +void BamToolsIndex::BamToolsIndexPrivate::KeepOnlyFirstReferenceOffsets(void) { + BamToolsIndexData::const_iterator indexBegin = m_indexData.begin(); + KeepOnlyReferenceOffsets( (*indexBegin).first ); +} + +// clears index data from all references except the one specified +void BamToolsIndex::BamToolsIndexPrivate::KeepOnlyReferenceOffsets(const int& refId) { + BamToolsIndexData::iterator mapIter = m_indexData.begin(); + BamToolsIndexData::iterator mapEnd = m_indexData.end(); + for ( ; mapIter != mapEnd; ++mapIter ) { + const int entryRefId = (*mapIter).first; + if ( entryRefId != refId ) + ClearReferenceOffsets(entryRefId); + } +} + +// load index data for all references, return true if loaded OK +bool BamToolsIndex::BamToolsIndexPrivate::LoadAllReferences(bool saveData) { + + // skip if data already loaded + if ( m_hasFullDataCache ) return true; + + // read in number of references + int32_t numReferences; + if ( !LoadReferenceCount(numReferences) ) return false; + //SetReferenceCount(numReferences); + + // iterate over reference entries + bool loadedOk = true; + for ( int i = 0; i < numReferences; ++i ) + loadedOk &= LoadReference(i, saveData); + + // set flag + if ( loadedOk && saveData ) + m_hasFullDataCache = true; + + // return success/failure of load + return loadedOk; +} + +// load header data from index file, return true if loaded OK +bool BamToolsIndex::BamToolsIndexPrivate::LoadHeader(void) { + + // check magic number + if ( !CheckMagicNumber() ) return false; + + // check BTI version + if ( !CheckVersion() ) 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); } + size_t elementsRead = fread(&m_blockSize, sizeof(m_blockSize), 1, m_parent->m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(m_blockSize); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_parent->m_indexStream); + + // return success/failure of load + return (elementsRead == 1); +} + +// load a single index entry from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamToolsIndex::BamToolsIndexPrivate::LoadIndexEntry(const int& refId, bool saveData) { - // reserve space for index data - d->m_indexData.reserve(numOffsets); + // read in index entry data members + size_t elementsRead = 0; + BamToolsIndexEntry entry; + elementsRead += fread(&entry.MaxEndPosition, sizeof(entry.MaxEndPosition), 1, m_parent->m_indexStream); + elementsRead += fread(&entry.StartOffset, sizeof(entry.StartOffset), 1, m_parent->m_indexStream); + elementsRead += fread(&entry.StartPosition, sizeof(entry.StartPosition), 1, m_parent->m_indexStream); + if ( elementsRead != 3 ) { + cerr << "Error reading index entry. Expected 3 elements, read in: " << elementsRead << endl; + return false; + } - // 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? + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(entry.MaxEndPosition); + SwapEndian_64(entry.StartOffset); + SwapEndian_32(entry.StartPosition); } - // close index file and return - fclose(indexStream); + // save data + if ( saveData ) + SaveOffsetEntry(refId, entry); + + // return success/failure of load 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) { +// load a single reference from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamToolsIndex::BamToolsIndexPrivate::LoadFirstReference(bool saveData) { + BamToolsIndexData::const_iterator indexBegin = m_indexData.begin(); + return LoadReference( (*indexBegin).first, saveData ); +} + +// load a single reference from file, return true if loaded OK +// @saveData - save data in memory if true, just read & discard if false +bool BamToolsIndex::BamToolsIndexPrivate::LoadReference(const int& refId, bool saveData) { + + // read in number of offsets for this reference + uint32_t numOffsets; + size_t elementsRead = fread(&numOffsets, sizeof(numOffsets), 1, m_parent->m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(numOffsets); - string indexFilename = bamFilename + ".bti"; - FILE* indexStream = fopen(indexFilename.c_str(), "wb"); - if ( indexStream == 0 ) { - fprintf(stderr, "ERROR: Could not open file to save index.\n"); - return false; + // initialize offsets container for this reference + SetOffsetCount(refId, (int)numOffsets); + + // iterate over offset entries + for ( unsigned int j = 0; j < numOffsets; ++j ) + LoadIndexEntry(refId, saveData); + + // return success/failure of load + return true; +} + +// loads number of references, return true if loaded OK +bool BamToolsIndex::BamToolsIndexPrivate::LoadReferenceCount(int& numReferences) { + + size_t elementsRead = 0; + + // read reference count + elementsRead += fread(&numReferences, sizeof(numReferences), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + + // return success/failure of load + return ( elementsRead == 1 ); +} + +// saves an index offset entry in memory +void BamToolsIndex::BamToolsIndexPrivate::SaveOffsetEntry(const int& refId, const BamToolsIndexEntry& entry) { + BamToolsReferenceEntry& refEntry = m_indexData[refId]; + refEntry.HasAlignments = true; + refEntry.Offsets.push_back(entry); +} + +// pre-allocates size for offset vector +void BamToolsIndex::BamToolsIndexPrivate::SetOffsetCount(const int& refId, const int& offsetCount) { + BamToolsReferenceEntry& refEntry = m_indexData[refId]; + refEntry.Offsets.reserve(offsetCount); + refEntry.HasAlignments = ( offsetCount > 0); +} + +// initializes index data structure to hold @count references +void BamToolsIndex::BamToolsIndexPrivate::SetReferenceCount(const int& count) { + for ( int i = 0; i < count; ++i ) + m_indexData[i].HasAlignments = false; +} + +// position file pointer to first reference begin, return true if skipped OK +bool BamToolsIndex::BamToolsIndexPrivate::SkipToFirstReference(void) { + BamToolsIndexData::const_iterator indexBegin = m_indexData.begin(); + return SkipToReference( (*indexBegin).first ); +} + +// position file pointer to desired reference begin, return true if skipped OK +bool BamToolsIndex::BamToolsIndexPrivate::SkipToReference(const int& refId) { + + // attempt rewind + if ( !m_parent->Rewind() ) return false; + + // read in number of references + int32_t numReferences; + size_t elementsRead = fread(&numReferences, sizeof(numReferences), 1, m_parent->m_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(numReferences); + + // iterate over reference entries + bool skippedOk = true; + int currentRefId = 0; + while (currentRefId != refId) { + skippedOk &= LoadReference(currentRefId, false); + ++currentRefId; } - // write BAM index header - fwrite("BTI\1", 1, 4, indexStream); + // return success/failure of skip + return skippedOk; +} + +// write header to new index file +bool BamToolsIndex::BamToolsIndexPrivate::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write BTI index format 'magic number' + elementsWritten += fwrite("BTI\1", 1, 4, m_parent->m_indexStream); + + // write BTI index format version + int32_t currentVersion = (int32_t)m_outputVersion; + if ( m_isBigEndian ) SwapEndian_32(currentVersion); + elementsWritten += fwrite(¤tVersion, sizeof(currentVersion), 1, m_parent->m_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); - + int32_t blockSize = m_blockSize; + if ( m_isBigEndian ) SwapEndian_32(blockSize); + elementsWritten += fwrite(&blockSize, sizeof(blockSize), 1, m_parent->m_indexStream); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_parent->m_indexStream); + + // return success/failure of write + return ( elementsWritten == 6 ); +} + +// write index data for all references to new index file +bool BamToolsIndex::BamToolsIndexPrivate::WriteAllReferences(void) { + + size_t elementsWritten = 0; + + // write number of references + int32_t numReferences = (int32_t)m_indexData.size(); + if ( m_isBigEndian ) SwapEndian_32(numReferences); + elementsWritten += fwrite(&numReferences, sizeof(numReferences), 1, m_parent->m_indexStream); + + // iterate through references in index + bool refOk = true; + BamToolsIndexData::const_iterator refIter = m_indexData.begin(); + BamToolsIndexData::const_iterator refEnd = m_indexData.end(); + for ( ; refIter != refEnd; ++refIter ) + refOk &= WriteReferenceEntry( (*refIter).second ); + + return ( (elementsWritten == 1) && refOk ); +} + +// write current reference index data to new index file +bool BamToolsIndex::BamToolsIndexPrivate::WriteReferenceEntry(const BamToolsReferenceEntry& refEntry) { + + size_t elementsWritten = 0; + + // write number of offsets listed for this reference + uint32_t numOffsets = refEntry.Offsets.size(); + if ( m_isBigEndian ) SwapEndian_32(numOffsets); + elementsWritten += fwrite(&numOffsets, sizeof(numOffsets), 1, m_parent->m_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 ) { + bool entriesOk = true; + vector::const_iterator offsetIter = refEntry.Offsets.begin(); + vector::const_iterator offsetEnd = refEntry.Offsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) + entriesOk &= WriteIndexEntry( (*offsetIter) ); - // 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); + return ( (elementsWritten == 1) && entriesOk ); +} + +// write current index offset entry to new index file +bool BamToolsIndex::BamToolsIndexPrivate::WriteIndexEntry(const BamToolsIndexEntry& entry) { + + // copy entry data + int32_t maxEndPosition = entry.MaxEndPosition; + int64_t startOffset = entry.StartOffset; + int32_t startPosition = entry.StartPosition; + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(maxEndPosition); + SwapEndian_64(startOffset); + SwapEndian_32(startPosition); } - // flush file buffer, close file, and return success - fflush(indexStream); - fclose(indexStream); - return true; + // write the reference index entry + size_t elementsWritten = 0; + elementsWritten += fwrite(&maxEndPosition, sizeof(maxEndPosition), 1, m_parent->m_indexStream); + elementsWritten += fwrite(&startOffset, sizeof(startOffset), 1, m_parent->m_indexStream); + elementsWritten += fwrite(&startPosition, sizeof(startPosition), 1, m_parent->m_indexStream); + return ( elementsWritten == 3 ); +} + +// --------------------------------------------------- +// BamToolsIndex implementation + +BamToolsIndex::BamToolsIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) +{ + d = new BamToolsIndexPrivate(this); +} + +BamToolsIndex::~BamToolsIndex(void) { + delete d; + d = 0; } + +// BamIndex interface implementation +bool BamToolsIndex::Build(void) { return d->Build(); } +void BamToolsIndex::ClearAllData(void) { d->ClearAllData(); } +const off_t BamToolsIndex::DataBeginOffset(void) const { return d->DataBeginOffset(); } +bool BamToolsIndex::HasAlignments(const int& referenceID) const { return d->HasAlignments(referenceID); } +bool BamToolsIndex::HasFullDataCache(void) const { return d->HasFullDataCache(); } +bool BamToolsIndex::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { return d->Jump(region, hasAlignmentsInRegion); } +void BamToolsIndex::KeepOnlyFirstReferenceOffsets(void) { d->KeepOnlyFirstReferenceOffsets(); } +bool BamToolsIndex::LoadAllReferences(bool saveData) { return d->LoadAllReferences(saveData); } +bool BamToolsIndex::LoadFirstReference(bool saveData) { return d->LoadFirstReference(saveData); } +bool BamToolsIndex::LoadHeader(void) { return d->LoadHeader(); } +bool BamToolsIndex::SkipToFirstReference(void) { return d->SkipToFirstReference(); } +bool BamToolsIndex::WriteAllReferences(void) { return d->WriteAllReferences(); } +bool BamToolsIndex::WriteHeader(void) { return d->WriteHeader(); }