X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamIndex.cpp;h=e72db5ff35c00c481347d6d5277b82d324e71f59;hb=0abdf800c25b306eb2f494d4f3516b598ae82b2d;hp=c628b793f3eb03b1c8f51f6671c98ff86ccbd266;hpb=1ec34c31512b530948037ebf34e072a50f0db5fa;p=bamtools.git diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp index c628b79..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: 10 September 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 @@ -24,24 +24,146 @@ 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; } // ######################################################################################### @@ -52,6 +174,10 @@ bool BamIndex::HasAlignments(const int& referenceID) { namespace BamTools { +// BAM index constants +const int MAX_BIN = 37450; // =(8^6-1)/7+1 +const int BAM_LIDX_SHIFT = 14; + // -------------------------------------------------- // BamStandardIndex data structures & typedefs struct Chunk { @@ -81,16 +207,19 @@ 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 BamStandardIndexData; +typedef map BamStandardIndexData; } // namespace BamTools @@ -99,49 +228,143 @@ typedef vector BamStandardIndexData; struct BamStandardIndex::BamStandardIndexPrivate { - // ------------------------- - // data members + // parent object + BamStandardIndex* m_parent; + // data members BamStandardIndexData m_indexData; - BamStandardIndex* m_parent; - - // ------------------------- - // ctor & dtor - - BamStandardIndexPrivate(BamStandardIndex* parent) : m_parent(parent) { } - ~BamStandardIndexPrivate(void) { m_indexData.clear(); } - - // ------------------------- - // 'public' methods + off_t m_dataBeginOffset; + bool m_hasFullDataCache; + bool m_isBigEndian; + + // ctor & dtor + BamStandardIndexPrivate(BamStandardIndex* parent); + ~BamStandardIndexPrivate(void); - // creates index data (in-memory) from current reader data - bool Build(void); - // attempts to use index to jump to region; returns success/fail - bool Jump(const BamTools::BamRegion& region); - // loads existing data from file into memory - bool Load(const std::string& filename); - // 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 Write(const std::string& bamFilename); + // 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 BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[BamTools::MAX_BIN]); - // calculates offset(s) for a given region - bool GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector& offsets); - // 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); + }; +BamStandardIndex::BamStandardIndexPrivate::BamStandardIndexPrivate(BamStandardIndex* parent) + : m_parent(parent) + , m_dataBeginOffset(0) + , m_hasFullDataCache(false) +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} + +BamStandardIndex::BamStandardIndexPrivate::~BamStandardIndexPrivate(void) { + ClearAllData(); +} + // calculate bins that overlap region -int BamStandardIndex::BamStandardIndexPrivate::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; @@ -171,13 +394,13 @@ int BamStandardIndex::BamStandardIndexPrivate::BinsFromRegion(const BamRegion& r return i; } +// 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; - RefVector& references = m_parent->m_references; // be sure reader & BGZF file are valid & open for reading if ( reader == 0 || mBGZF == 0 || !mBGZF->IsOpen ) @@ -187,9 +410,10 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { reader->Rewind(); // get reference count, reserve index space - int numReferences = (int)references.size(); - for ( int i = 0; i < numReferences; ++i ) - 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; @@ -221,7 +445,8 @@ bool BamStandardIndex::BamStandardIndexPrivate::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); } @@ -229,9 +454,11 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) { // save linear offset entry (matched to BAM entry refID) - ReferenceIndex& refIndex = 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; - InsertLinearOffset(offsets, bAlignment, lastOffset); + SaveLinearOffset(offsets, bAlignment, lastOffset); } // if current BamAlignment bin != lastBin, "then possibly write the binning index" @@ -241,9 +468,11 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { if ( saveBin != defaultValue ) { // save Bam bin entry - ReferenceIndex& refIndex = 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; - InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); } // update saveOffset @@ -276,29 +505,26 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { // save any leftover BAM data (as long as refID is valid) if ( saveRefID >= 0 ) { // save Bam bin entry - ReferenceIndex& refIndex = 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; - InsertBinEntry(binMap, saveBin, saveOffset, lastOffset); + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); } // simplify index by merging chunks MergeChunks(); - + // iterate through references in index - // store whether reference has data & // sort offsets in linear offset vector 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 - references[i].RefHasAlignments = ( binMap.size() > 0 ); - // sort linear offsets sort(offsets.begin(), offsets.end()); } @@ -307,19 +533,87 @@ bool BamStandardIndex::BamStandardIndexPrivate::Build(void) { return reader->Rewind(); } -bool BamStandardIndex::BamStandardIndexPrivate::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 = BinsFromRegion(region, isRightBoundSpecified, bins); // get bins for this reference - const ReferenceIndex& refIndex = 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 ) { @@ -348,79 +642,69 @@ bool BamStandardIndex::BamStandardIndexPrivate::GetOffsets(const BamRegion& regi // 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 BamStandardIndex::BamStandardIndexPrivate::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 BamStandardIndex::BamStandardIndexPrivate::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; -bool BamStandardIndex::BamStandardIndexPrivate::Jump(const BamRegion& region) { + // return whether bin map contains data + return ( !refEntry.Bins.empty() ); +} + +// 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; + 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; - // see if left-bound reference of region has alignments - if ( !m_parent->HasAlignments(region.LeftRefID) ) return false; - // make sure left-bound position is valid - if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) return false; + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) + return false; + // calculate offsets for this region + // if failed, print message, set flag, and return failure vector offsets; - if ( !GetOffsets(region, region.isRightBoundSpecified(), offsets) ) { - fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n"); + 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; } @@ -430,147 +714,248 @@ bool BamStandardIndex::BamStandardIndexPrivate::Jump(const BamRegion& region) { 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); - reader->GetNextAlignmentCore(bAlignment); + *hasAlignmentsInRegion = reader->GetNextAlignmentCore(bAlignment); // if this alignment corresponds to desired position - // return success of seeking back to 'current offset' - if ( (bAlignment.RefID == region.LeftRefID && bAlignment.Position + bAlignment.Length > region.LeftPosition) || (bAlignment.RefID > region.LeftRefID) ) { + // 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 ( !result ) fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n"); + // 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; } -bool BamStandardIndex::BamStandardIndexPrivate::Load(const string& filename) { - - // localize parent data - if ( m_parent == 0 ) return false; - const bool isBigEndian = m_parent->m_isBigEndian; - RefVector& references = m_parent->m_references; - - // 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()); - return false; +// 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); } +} - // 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); +bool BamStandardIndex::BamStandardIndexPrivate::LoadAllReferences(bool saveData) { + + // skip if data already loaded + if ( m_hasFullDataCache ) return true; + + // get number of reference sequences + uint32_t numReferences; + if ( !LoadReferenceCount((int&)numReferences) ) return false; + + // iterate over reference entries + bool loadedOk = true; + for ( int i = 0; i < (int)numReferences; ++i ) + loadedOk &= LoadReference(i, saveData); + + // set flag + if ( loadedOk && saveData ) + m_hasFullDataCache = true; + + // return success/failure of loading references + return loadedOk; +} + +// load header data from index file, return true if loaded OK +bool BamStandardIndex::BamStandardIndexPrivate::LoadHeader(void) { + + bool loadedOk = CheckMagicNumber(); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_parent->m_indexStream); + + // return success/failure of load + return loadedOk; +} + +// 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) { + + size_t elementsRead = 0; + + // get bin ID + uint32_t binId; + elementsRead += fread(&binId, sizeof(binId), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(binId); + + // load alignment chunks for this bin + ChunkVector chunks; + bool chunksOk = LoadChunks(chunks, saveData); + + // store bin entry + if ( chunksOk && saveData ) + refEntry.Bins.insert(pair(binId, chunks)); + + // return success/failure of load + return ( (elementsRead == 1) && chunksOk ); +} + +bool BamStandardIndex::BamStandardIndexPrivate::LoadBins(ReferenceIndex& refEntry, bool saveData) { + + 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; + + // 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); } - // get number of reference sequences - uint32_t numRefSeqs; - elementsRead = fread(&numRefSeqs, 4, 1, indexStream); - if ( isBigEndian ) SwapEndian_32(numRefSeqs); - - // intialize space for BamStandardIndexData data structure - m_indexData.reserve(numRefSeqs); + // save data if requested + if ( saveData ) chunks.push_back( Chunk(start, stop) ); - // iterate over reference sequences - for ( unsigned int i = 0; i < numRefSeqs; ++i ) { + // return success/failure of load + return ( elementsRead == 2 ); +} - // get number of bins for this reference sequence - int32_t numBins; - elementsRead = fread(&numBins, 4, 1, indexStream); - if ( isBigEndian ) SwapEndian_32(numBins); +bool BamStandardIndex::BamStandardIndexPrivate::LoadChunks(ChunkVector& chunks, bool saveData) { - if ( numBins > 0 ) { - RefData& refEntry = references[i]; - refEntry.RefHasAlignments = true; - } + size_t elementsRead = 0; - // intialize BinVector - BamBinMap binMap; + // read in number of chunks + uint32_t numChunks; + elementsRead += fread(&numChunks, sizeof(numChunks), 1, m_parent->m_indexStream); + if ( m_isBigEndian ) SwapEndian_32(numChunks); - // iterate over bins for that reference sequence - for ( int j = 0; j < numBins; ++j ) { + // initialize space for chunks if we're storing this data + if ( saveData ) chunks.reserve(numChunks); - // get binID - uint32_t binID; - elementsRead = fread(&binID, 4, 1, indexStream); + // iterate over chunks + bool chunksOk = true; + for ( int i = 0; i < (int)numChunks; ++i ) + chunksOk &= LoadChunk(chunks, saveData); - // get number of regionChunks in this bin - uint32_t numChunks; - elementsRead = fread(&numChunks, 4, 1, indexStream); + // sort chunk vector + sort( chunks.begin(), chunks.end(), ChunkLessThan ); - if ( 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 ( isBigEndian ) { - SwapEndian_64(left); - SwapEndian_64(right); - } - - // save ChunkPair - regionChunks.push_back( Chunk(left, right) ); - } + // return success/failure of load + return ( (elementsRead == 1) && chunksOk ); +} - // sort chunks for this bin - sort( regionChunks.begin(), regionChunks.end(), ChunkLessThan ); +// 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) { - // save binID, chunkVector for this bin - binMap.insert( pair(binID, regionChunks) ); - } + size_t elementsRead = 0; - // ----------------------------------------------------- - // load linear index for this reference sequence - - // get number of linear offsets - int32_t numLinearOffsets; - elementsRead = fread(&numLinearOffsets, 4, 1, indexStream); - if ( 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 ( isBigEndian ) SwapEndian_64(linearOffset); - offsets.push_back(linearOffset); - } + // 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( offsets.begin(), offsets.end() ); + // 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) ); +} - // store index data for that reference sequence - m_indexData.push_back( ReferenceIndex(binMap, offsets) ); +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) ); } - // close index file (.bai) and return - fclose(indexStream); - return true; + // 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) @@ -582,7 +967,7 @@ void BamStandardIndex::BamStandardIndexPrivate::MergeChunks(void) { 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 @@ -609,12 +994,9 @@ void BamStandardIndex::BamStandardIndexPrivate::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 { @@ -630,111 +1012,245 @@ void BamStandardIndex::BamStandardIndexPrivate::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 BamStandardIndex::BamStandardIndexPrivate::Write(const std::string& bamFilename) { +// 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); - // localize parent data - if ( m_parent == 0 ) return false; - const bool isBigEndian = m_parent->m_isBigEndian; - - 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; - } + // create new chunk + Chunk newChunk(saveOffset, lastOffset); - // write BAM index header - fwrite("BAI\1", 1, 4, indexStream); + // if entry doesn't exist + if ( binIter == binMap.end() ) { + ChunkVector newChunks; + newChunks.push_back(newChunk); + binMap.insert( pair(saveBin, newChunks)); + } - // write number of reference sequences - int32_t numReferenceSeqs = m_indexData.size(); - if ( isBigEndian ) SwapEndian_32(numReferenceSeqs); - fwrite(&numReferenceSeqs, 4, 1, indexStream); + // otherwise + else { + ChunkVector& binChunks = (*binIter).second; + binChunks.push_back( newChunk ); + } +} - // iterate over reference sequences +// 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; + + // 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; + } +} + +// 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; +} + +bool BamStandardIndex::BamStandardIndexPrivate::SkipToFirstReference(void) { + BamStandardIndexData::const_iterator indexBegin = m_indexData.begin(); + return SkipToReference( (*indexBegin).first ); +} + +// position file pointer to desired reference begin, return true if skipped OK +bool BamStandardIndex::BamStandardIndexPrivate::SkipToReference(const int& refId) { + + // attempt rewind + if ( !m_parent->Rewind() ) return false; + + // 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; + } + + // 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 ) { + for ( ; indexIter != indexEnd; ++ indexIter ) + refsOk &= WriteReference( (*indexIter).second ); - // 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 ( 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 ) { + // return success/failure of write + return ( (elementsWritten == 1) && refsOk ); +} - // get bin data (key and chunk vector) - uint32_t binKey = (*binIter).first; - const ChunkVector& binChunks = (*binIter).second; +// write index data for bin to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteBin(const uint32_t& binId, const ChunkVector& chunks) { - // save BAM bin key - if ( isBigEndian ) SwapEndian_32(binKey); - fwrite(&binKey, 4, 1, indexStream); + size_t elementsWritten = 0; - // save chunk count - int32_t chunkCount = binChunks.size(); - if ( isBigEndian ) SwapEndian_32(chunkCount); - fwrite(&chunkCount, 4, 1, indexStream); + // write BAM bin ID + uint32_t binKey = binId; + if ( m_isBigEndian ) SwapEndian_32(binKey); + elementsWritten += fwrite(&binKey, sizeof(binKey), 1, m_parent->m_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 ( isBigEndian ) { - SwapEndian_64(start); - SwapEndian_64(stop); - } - - // save chunk offsets - fwrite(&start, 8, 1, indexStream); - fwrite(&stop, 8, 1, indexStream); - } - } + // write chunks + bool chunksOk = WriteChunks(chunks); - // write linear offsets size - int32_t offsetSize = offsets.size(); - if ( isBigEndian ) SwapEndian_32(offsetSize); - fwrite(&offsetSize, 4, 1, indexStream); + // return success/failure of write + return ( (elementsWritten == 1) && chunksOk ); +} - // iterate over linear offsets - LinearOffsetVector::const_iterator offsetIter = offsets.begin(); - LinearOffsetVector::const_iterator offsetEnd = offsets.end(); - for ( ; offsetIter != offsetEnd; ++offsetIter ) { +// write index data for bins to new index file +bool BamStandardIndex::BamStandardIndexPrivate::WriteBins(const BamBinMap& bins) { - // write linear offset value - uint64_t linearOffset = (*offsetIter); - if ( isBigEndian ) SwapEndian_64(linearOffset); - fwrite(&linearOffset, 8, 1, indexStream); - } + 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); } - // flush buffer, close file, and return success - fflush(indexStream); - fclose(indexStream); - return true; + // 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, bool isBigEndian) - : BamIndex(bgzf, reader, isBigEndian) +BamStandardIndex::BamStandardIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) { d = new BamStandardIndexPrivate(this); } @@ -744,18 +1260,20 @@ BamStandardIndex::~BamStandardIndex(void) { d = 0; } -// creates index data (in-memory) from current reader data +// BamIndex interface implementation bool BamStandardIndex::Build(void) { return d->Build(); } - -// attempts to use index to jump to region; returns success/fail -bool BamStandardIndex::Jump(const BamRegion& region) { return d->Jump(region); } - -// loads existing data from file into memory -bool BamStandardIndex::Load(const string& filename) { return d->Load(filename); } - -// 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 BamStandardIndex::Write(const string& bamFilename) { return d->Write(bamFilename); } +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(); } // ######################################################################################### // ######################################################################################### @@ -765,7 +1283,7 @@ bool BamStandardIndex::Write(const string& bamFilename) { return d->Write(bamFil namespace BamTools { -// individual index entry +// individual index offset entry struct BamToolsIndexEntry { // data members @@ -783,8 +1301,21 @@ struct BamToolsIndexEntry { { } }; +// reference index entry +struct BamToolsReferenceEntry { + + // data members + bool HasAlignments; + vector Offsets; + + // ctor + BamToolsReferenceEntry(void) + : HasAlignments(false) + { } +}; + // the actual index data structure -typedef map > BamToolsIndexData; +typedef map BamToolsIndexData; } // namespace BamTools @@ -795,7 +1326,7 @@ 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_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on + // 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: // @@ -803,65 +1334,148 @@ struct BamToolsIndex::BamToolsIndexPrivate { // do something new // else // do the old thing - enum Version { BTI_1_0 = 1 }; + 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; - Version m_version; - - // ------------------------- - // ctor & dtor - - BamToolsIndexPrivate(BamToolsIndex* parent) - : m_parent(parent) - , m_blockSize(1000) - , m_version(BTI_1_0) // latest version - used for writing new index files - { } - - ~BamToolsIndexPrivate(void) { } + 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; - // ------------------------- - // 'public' methods + // ctor & dtor + BamToolsIndexPrivate(BamToolsIndex* parent); + ~BamToolsIndexPrivate(void); - // creates index data (in-memory) from current reader data - bool Build(void); - // returns supported file extension - const std::string Extension(void) const { return std::string(".bti"); } - // attempts to use index to jump to region; returns success/fail - bool Jump(const BamTools::BamRegion& region); - // loads existing data from file into memory - bool Load(const std::string& filename); - // 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 Write(const std::string& bamFilename); + // 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 - - // calculates offset for a given region - bool GetOffset(const BamRegion& region, int64_t& offset); + 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); }; +// 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(); +} + +// dtor +BamToolsIndex::BamToolsIndexPrivate::~BamToolsIndexPrivate(void) { + ClearAllData(); +} + +// 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; - 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; // move file pointer to beginning of alignments - // quit if failed - if ( !reader->Rewind() ) - return false; + 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(); @@ -877,13 +1491,11 @@ bool BamToolsIndex::BamToolsIndexPrivate::Build(void) { // if block contains data (not the first time through) AND alignment is on a new reference if ( currentBlockCount > 0 && al.RefID != blockRefId ) { - // make sure reference flag is set - references[blockRefId].RefHasAlignments = true; - - // store previous data - m_indexData[blockRefId].push_back( BamToolsIndexEntry(blockMaxEndPosition, blockStartOffset, blockStartPosition) ); - - // intialize new block + // 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; @@ -897,7 +1509,7 @@ bool BamToolsIndex::BamToolsIndexPrivate::Build(void) { // increment block counter ++currentBlockCount; - + // check end position int32_t alignmentEndPosition = al.GetEndPosition(); if ( alignmentEndPosition > blockMaxEndPosition ) @@ -905,11 +1517,8 @@ bool BamToolsIndex::BamToolsIndexPrivate::Build(void) { // if block is full, get offset for next block, reset currentBlockCount if ( currentBlockCount == m_blockSize ) { - - // make sure reference flag is set - references[blockRefId].RefHasAlignments = true; - - m_indexData[blockRefId].push_back( BamToolsIndexEntry(blockMaxEndPosition, blockStartOffset, blockStartPosition) ); + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); blockStartOffset = mBGZF->Tell(); currentBlockCount = 0; } @@ -919,247 +1528,487 @@ bool BamToolsIndex::BamToolsIndexPrivate::Build(void) { currentAlignmentOffset = mBGZF->Tell(); } - // attempt to rewind back to begnning of alignments - // return success/fail + // 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(); } +// 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 BamToolsIndex::BamToolsIndexPrivate::GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion) { // return false if leftBound refID is not found in index data - if ( m_indexData.find(region.LeftRefID) == m_indexData.end() ) return false; - - const vector referenceOffsets = m_indexData[region.LeftRefID]; + 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 // save first offset offset = (*referenceOffsets.begin()).StartOffset; - vector::const_iterator indexIter = referenceOffsets.begin(); - vector::const_iterator indexEnd = referenceOffsets.end(); - for ( ; indexIter != indexEnd; ++indexIter ) { - const BamToolsIndexEntry& entry = (*indexIter); + + // 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 = (*indexIter).StartOffset; + offset = (*offsetIter).StartOffset; } - // no index found - if ( indexIter == indexEnd ) return false; - - // return succes + // 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::BamToolsIndexPrivate::Jump(const BamRegion& region) { +// 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) { + + // 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; + 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; } - // see if left-bound reference of region has alignments - if ( !m_parent->HasAlignments(region.LeftRefID) ) return false; - // make sure left-bound position is valid - if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) return false; + if ( region.LeftPosition > references.at(region.LeftRefID).RefLength ) + return false; // calculate nearest offset to jump to int64_t offset; - if ( !GetOffset(region, offset) ) { + if ( !GetOffset(region, offset, hasAlignmentsInRegion) ) { fprintf(stderr, "ERROR: Could not jump - unable to calculate offset for specified region.\n"); return false; } - - // attempt seek in file, return success/fail + + // return success/failure of seek return mBGZF->Seek(offset); } -bool BamToolsIndex::BamToolsIndexPrivate::Load(const string& filename) { - - // localize parent data - if ( m_parent == 0 ) return false; - const bool isBigEndian = m_parent->m_isBigEndian; - RefVector& references = m_parent->m_references; - - // 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()); - return false; +// 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 + 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); - // set placeholder to receive input byte count (suppresses compiler warnings) + // 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) { + + // read in index entry data members 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); + 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; } - // read in version - int32_t indexVersion; - elementsRead = fread(&indexVersion, sizeof(indexVersion), 1, indexStream); - if ( isBigEndian ) SwapEndian_32(indexVersion); - if ( indexVersion <= 0 || indexVersion > m_version ) { - fprintf(stderr, "Problem with index file - unsupported version.\n"); - fclose(indexStream); - return false; + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(entry.MaxEndPosition); + SwapEndian_64(entry.StartOffset); + SwapEndian_32(entry.StartPosition); } - // read in block size - elementsRead = fread(&m_blockSize, sizeof(m_blockSize), 1, indexStream); - if ( isBigEndian ) SwapEndian_32(m_blockSize); + // save data + if ( saveData ) + SaveOffsetEntry(refId, entry); + + // return success/failure of load + return 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 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); + + // 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; - elementsRead = fread(&numReferences, sizeof(numReferences), 1, indexStream); - if ( isBigEndian ) SwapEndian_32(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 - for ( int i = 0; i < numReferences; ++i ) { - - // read in number of offsets for this reference - uint32_t numOffsets; - elementsRead = fread(&numOffsets, sizeof(numOffsets), 1, indexStream); - if ( isBigEndian ) SwapEndian_32(numOffsets); - - // initialize offsets container for this reference - vector offsets; - offsets.reserve(numOffsets); - - // iterate over offset entries - for ( unsigned int j = 0; j < numOffsets; ++j ) { - - // copy entry data - int32_t maxEndPosition; - int64_t startOffset; - int32_t startPosition; - - // read in data - elementsRead = fread(&maxEndPosition, sizeof(maxEndPosition), 1, indexStream); - elementsRead = fread(&startOffset, sizeof(startOffset), 1, indexStream); - elementsRead = fread(&startPosition, sizeof(startPosition), 1, indexStream); - - // swap endian-ness if necessary - if ( isBigEndian ) { - SwapEndian_32(maxEndPosition); - SwapEndian_64(startOffset); - SwapEndian_32(startPosition); - } - - // save current index entry - offsets.push_back( BamToolsIndexEntry(maxEndPosition, startOffset, startPosition) ); - } - - // save refID, offsetVector entry into data structure - m_indexData.insert( make_pair(i, offsets) ); - - // set ref.HasAlignments flag - references[i].RefHasAlignments = (numOffsets != 0); + bool skippedOk = true; + int currentRefId = 0; + while (currentRefId != refId) { + skippedOk &= LoadReference(currentRefId, false); + ++currentRefId; } - // close index file and return - fclose(indexStream); - return true; + // return success/failure of skip + return skippedOk; } -// 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::BamToolsIndexPrivate::Write(const std::string& bamFilename) { - - // localize parent data - if ( m_parent == 0 ) return false; - const bool isBigEndian = m_parent->m_isBigEndian; - - // open index file for writing - 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; - } +// write header to new index file +bool BamToolsIndex::BamToolsIndexPrivate::WriteHeader(void) { + + size_t elementsWritten = 0; // write BTI index format 'magic number' - fwrite("BTI\1", 1, 4, indexStream); + elementsWritten += fwrite("BTI\1", 1, 4, m_parent->m_indexStream); // write BTI index format version - int32_t currentVersion = (int32_t)m_version; - if ( isBigEndian ) SwapEndian_32(currentVersion); - fwrite(¤tVersion, sizeof(int32_t), 1, indexStream); - + 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 = m_blockSize; - if ( isBigEndian ) SwapEndian_32(blockSize); - fwrite(&blockSize, sizeof(blockSize), 1, indexStream); - + 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 ( isBigEndian ) SwapEndian_32(numReferences); - fwrite(&numReferences, sizeof(numReferences), 1, indexStream); - - // iterate through references in index + 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 ) { - - const vector offsets = (*refIter).second; - - // write number of offsets listed for this reference - uint32_t numOffsets = offsets.size(); - if ( isBigEndian ) SwapEndian_32(numOffsets); - fwrite(&numOffsets, sizeof(numOffsets), 1, indexStream); - - // iterate over offset entries - vector::const_iterator offsetIter = offsets.begin(); - vector::const_iterator offsetEnd = offsets.end(); - for ( ; offsetIter != offsetEnd; ++offsetIter ) { - - // get reference index data - const BamToolsIndexEntry& entry = (*offsetIter); - - // copy entry data - int32_t maxEndPosition = entry.MaxEndPosition; - int64_t startOffset = entry.StartOffset; - int32_t startPosition = entry.StartPosition; - - // swap endian-ness if necessary - if ( isBigEndian ) { - SwapEndian_32(maxEndPosition); - SwapEndian_64(startOffset); - SwapEndian_32(startPosition); - } - - // write the reference index entry - fwrite(&maxEndPosition, sizeof(maxEndPosition), 1, indexStream); - fwrite(&startOffset, sizeof(startOffset), 1, indexStream); - fwrite(&startPosition, sizeof(startPosition), 1, indexStream); - } + 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 + bool entriesOk = true; + vector::const_iterator offsetIter = refEntry.Offsets.begin(); + vector::const_iterator offsetEnd = refEntry.Offsets.end(); + for ( ; offsetIter != offsetEnd; ++offsetIter ) + entriesOk &= WriteIndexEntry( (*offsetIter) ); + + 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 any remaining output, 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, bool isBigEndian) - : BamIndex(bgzf, reader, isBigEndian) +BamToolsIndex::BamToolsIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) { d = new BamToolsIndexPrivate(this); } @@ -1169,15 +2018,17 @@ BamToolsIndex::~BamToolsIndex(void) { d = 0; } -// creates index data (in-memory) from current reader data +// BamIndex interface implementation bool BamToolsIndex::Build(void) { return d->Build(); } - -// attempts to use index to jump to region; returns success/fail -bool BamToolsIndex::Jump(const BamRegion& region) { return d->Jump(region); } - -// loads existing data from file into memory -bool BamToolsIndex::Load(const string& filename) { return d->Load(filename); } - -// 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 string& bamFilename) { return d->Write(bamFilename); } +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(); }