From 6f3fff23561d95067651931a8768c6466cabe99f Mon Sep 17 00:00:00 2001 From: derek Date: Fri, 19 Nov 2010 15:52:04 -0500 Subject: [PATCH] Continued breaking up of monolithic classes: extracted BamStandardIndex & BamToolsIndex into their own source files. --- src/api/BamIndex.cpp | 1929 ++-------------------------------- src/api/BamIndex.h | 184 +--- src/api/BamReader_p.cpp | 3 + src/api/BamStandardIndex.cpp | 910 ++++++++++++++++ src/api/BamStandardIndex.h | 213 ++++ src/api/BamToolsIndex.cpp | 577 ++++++++++ src/api/BamToolsIndex.h | 192 ++++ src/api/BamWriter_p.cpp | 2 +- src/api/CMakeLists.txt | 2 + 9 files changed, 1970 insertions(+), 2042 deletions(-) create mode 100644 src/api/BamStandardIndex.cpp create mode 100644 src/api/BamStandardIndex.h create mode 100644 src/api/BamToolsIndex.cpp create mode 100644 src/api/BamToolsIndex.h diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp index ae5a463..053f8e9 100644 --- a/src/api/BamIndex.cpp +++ b/src/api/BamIndex.cpp @@ -13,7 +13,10 @@ #include #include #include +#include +#include using namespace BamTools; +using namespace BamTools::Internal; #include #include @@ -22,6 +25,65 @@ using namespace BamTools; #include using namespace std; +// -------------------------------------------------- +// BamIndex factory methods + +// returns index based on BAM filename 'stub' +// checks first for preferred type, returns that type if found +// (if not found, attmempts to load other type(s), returns 0 if NONE found) +// +// ** default preferred type is BamToolsIndex ** use this anytime it exists +BamIndex* BamIndex::FromBamFilename(const std::string& bamFilename, + BamTools::BgzfData* bgzf, + BamTools::BamReader* reader, + const BamIndex::PreferredIndexType& type) +{ + // --------------------------------------------------- + // attempt to load preferred type first + + const std::string bamtoolsIndexFilename = bamFilename + ".bti"; + const bool bamtoolsIndexExists = BamTools::FileExists(bamtoolsIndexFilename); + if ( (type == BamIndex::BAMTOOLS) && bamtoolsIndexExists ) + return new BamToolsIndex(bgzf, reader); + + const std::string standardIndexFilename = bamFilename + ".bai"; + const bool standardIndexExists = BamTools::FileExists(standardIndexFilename); + if ( (type == BamIndex::STANDARD) && standardIndexExists ) + return new BamStandardIndex(bgzf, reader); + + // ---------------------------------------------------- + // preferred type could not be found, try other (non-preferred) types + // if none found, return 0 + + if ( bamtoolsIndexExists ) return new BamToolsIndex(bgzf, reader); + if ( standardIndexExists ) return new BamStandardIndex(bgzf, reader); + return 0; +} + +// returns index based on explicitly named index file (or 0 if not found) +BamIndex* BamIndex::FromIndexFilename(const std::string& indexFilename, + BamTools::BgzfData* bgzf, + BamTools::BamReader* reader) +{ + // see if specified file exists + const bool indexExists = BamTools::FileExists(indexFilename); + if ( !indexExists ) return 0; + + const std::string bamtoolsIndexExtension(".bti"); + const std::string standardIndexExtension(".bai"); + + // if has bamtoolsIndexExtension + if ( indexFilename.find(bamtoolsIndexExtension) == (indexFilename.length() - bamtoolsIndexExtension.length()) ) + return new BamToolsIndex(bgzf, reader); + + // if has standardIndexExtension + if ( indexFilename.find(standardIndexExtension) == (indexFilename.length() - standardIndexExtension.length()) ) + return new BamStandardIndex(bgzf, reader); + + // otherwise, unsupported file type + return 0; +} + // ------------------------------- // BamIndex implementation @@ -166,1870 +228,3 @@ bool BamIndex::Write(const string& bamFilename) { // return success/failure of write return true; } - -// ######################################################################################### -// ######################################################################################### - -// ------------------------------- -// BamStandardIndex structs & typedefs - -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 { - - // data members - uint64_t Start; - uint64_t Stop; - - // constructor - Chunk(const uint64_t& start = 0, - const uint64_t& stop = 0) - : Start(start) - , Stop(stop) - { } -}; - -bool ChunkLessThan(const Chunk& lhs, const Chunk& rhs) { - return lhs.Start < rhs.Start; -} - -typedef vector ChunkVector; -typedef map BamBinMap; -typedef vector LinearOffsetVector; - -struct ReferenceIndex { - - // data members - BamBinMap Bins; - LinearOffsetVector Offsets; - bool HasAlignments; - - // constructor - ReferenceIndex(const BamBinMap& binMap = BamBinMap(), - const LinearOffsetVector& offsets = LinearOffsetVector(), - const bool hasAlignments = false) - : Bins(binMap) - , Offsets(offsets) - , HasAlignments(hasAlignments) - { } -}; - -typedef map BamStandardIndexData; - -} // namespace BamTools - -// ------------------------------- -// BamStandardIndexPrivate implementation - -struct BamStandardIndex::BamStandardIndexPrivate { - - // parent object - BamStandardIndex* m_parent; - - // data members - BamStandardIndexData m_indexData; - off_t m_dataBeginOffset; - bool m_hasFullDataCache; - bool m_isBigEndian; - - // ctor & dtor - BamStandardIndexPrivate(BamStandardIndex* parent); - ~BamStandardIndexPrivate(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 - 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]) -{ - // get region boundaries - uint32_t begin = (unsigned int)region.LeftPosition; - uint32_t end; - - // if right bound specified AND left&right bounds are on same reference - // OK to use right bound position - if ( isRightBoundSpecified && ( region.LeftRefID == region.RightRefID ) ) - end = (unsigned int)region.RightPosition; - - // otherwise, use end of left bound reference as cutoff - else - end = (unsigned int)m_parent->m_references.at(region.LeftRefID).RefLength - 1; - - // initialize list, bin '0' always a valid bin - int i = 0; - bins[i++] = 0; - - // get rest of bins that contain this region - unsigned int k; - for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { bins[i++] = k; } - for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { bins[i++] = k; } - for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { bins[i++] = k; } - for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { bins[i++] = k; } - for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { bins[i++] = k; } - - // return number of bins stored - return i; -} - -// 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 ( reader == 0 || mBGZF == 0 || !mBGZF->IsOpen ) - return false; - - // move file pointer to beginning of alignments - reader->Rewind(); - - // get reference count, reserve index space - 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; - - // bin data - uint32_t saveBin(defaultValue); - uint32_t lastBin(defaultValue); - - // reference ID data - int32_t saveRefID(defaultValue); - int32_t lastRefID(defaultValue); - - // offset data - uint64_t saveOffset = mBGZF->Tell(); - uint64_t lastOffset = saveOffset; - - // coordinate data - int32_t lastCoordinate = defaultValue; - - BamAlignment bAlignment; - while ( reader->GetNextAlignmentCore(bAlignment) ) { - - // change of chromosome, save ID, reset bin - if ( lastRefID != bAlignment.RefID ) { - lastRefID = bAlignment.RefID; - lastBin = defaultValue; - } - - // if lastCoordinate greater than BAM position - file not sorted properly - else if ( lastCoordinate > bAlignment.Position ) { - 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); - exit(1); - } - - // if valid reference && BAM bin spans some minimum cutoff (smaller bin ids span larger regions) - if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) { - - // save linear offset entry (matched to BAM entry refID) - BamStandardIndexData::iterator indexIter = m_indexData.find(bAlignment.RefID); - if ( indexIter == m_indexData.end() ) return false; // error - ReferenceIndex& refIndex = (*indexIter).second; - LinearOffsetVector& offsets = refIndex.Offsets; - SaveLinearOffset(offsets, bAlignment, lastOffset); - } - - // if current BamAlignment bin != lastBin, "then possibly write the binning index" - if ( bAlignment.Bin != lastBin ) { - - // if not first time through - if ( saveBin != defaultValue ) { - - // save Bam bin entry - BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); - if ( indexIter == m_indexData.end() ) return false; // error - ReferenceIndex& refIndex = (*indexIter).second; - BamBinMap& binMap = refIndex.Bins; - SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); - } - - // update saveOffset - saveOffset = lastOffset; - - // update bin values - saveBin = bAlignment.Bin; - lastBin = bAlignment.Bin; - - // update saveRefID - saveRefID = bAlignment.RefID; - - // if invalid RefID, break out - if ( saveRefID < 0 ) break; - } - - // make sure that current file pointer is beyond lastOffset - if ( mBGZF->Tell() <= (int64_t)lastOffset ) { - fprintf(stderr, "Error in BGZF offsets.\n"); - exit(1); - } - - // update lastOffset - lastOffset = mBGZF->Tell(); - - // update lastCoordinate - lastCoordinate = bAlignment.Position; - } - - // save any leftover BAM data (as long as refID is valid) - if ( saveRefID >= 0 ) { - // save Bam bin entry - BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); - if ( indexIter == m_indexData.end() ) return false; // error - ReferenceIndex& refIndex = (*indexIter).second; - BamBinMap& binMap = refIndex.Bins; - SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); - } - - // simplify index by merging chunks - MergeChunks(); - - // iterate through references in index - // 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).second; - LinearOffsetVector& offsets = refIndex.Offsets; - - // sort linear offsets - sort(offsets.begin(), offsets.end()); - } - - // rewind file pointer to beginning of alignments, return success/fail - return reader->Rewind(); -} - -// 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 - 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; - 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 ) { - - const uint16_t binKey = bins[i]; - 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(); - for ( ; chunksIter != chunksEnd; ++chunksIter) { - - // if valid chunk found, store its file offset - const Chunk& chunk = (*chunksIter); - if ( chunk.Stop > minOffset ) - offsets.push_back( chunk.Start ); - } - } - } - - // clean up memory - free(bins); - - // sort the offsets before returning - sort(offsets.begin(), offsets.end()); - - // set flag & return success - *hasAlignmentsInRegion = (offsets.size() != 0 ); - - // if cache mode set to none, dump the data we just loaded - if (m_parent->m_cacheMode == BamIndex::NoIndexCaching ) - ClearReferenceOffsets(region.LeftRefID); - - // return succes - return true; -} - -// 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; -} - -// return true if all index data is cached -bool BamStandardIndex::BamStandardIndexPrivate::HasFullDataCache(void) const { - return m_hasFullDataCache; -} - -// returns true if index cache has data for desired reference -bool BamStandardIndex::BamStandardIndexPrivate::IsDataLoaded(const int& refId) const { - - // look up refId, return false if not found - BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId); - if ( indexIter == m_indexData.end() ) return false; - - // 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() ); -} - -// 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; - - // make sure left-bound position is valid - 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, 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 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); - } - - // 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 BamStandardIndex::BamStandardIndexPrivate::MergeChunks(void) { - - // iterate over reference enties - 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).second; - BamBinMap& bamBinMap = refIndex.Bins; - - // iterate over BAM bins - BamBinMap::iterator binIter = bamBinMap.begin(); - BamBinMap::iterator binEnd = bamBinMap.end(); - for ( ; binIter != binEnd; ++binIter ) { - - // get chunk vector for this bin - ChunkVector& binChunks = (*binIter).second; - if ( binChunks.size() == 0 ) continue; - - ChunkVector mergedChunks; - mergedChunks.push_back( binChunks[0] ); - - // iterate over chunks - int i = 0; - ChunkVector::iterator chunkIter = binChunks.begin(); - ChunkVector::iterator chunkEnd = binChunks.end(); - for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) { - - // get 'currentChunk' based on numeric index - Chunk& currentChunk = mergedChunks[i]; - - // get iteratorChunk based on vector iterator - Chunk& iteratorChunk = (*chunkIter); - - // if chunk ends where (iterator) chunk starts, then merge - if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) - currentChunk.Stop = iteratorChunk.Stop; - - // otherwise - else { - // set currentChunk + 1 to iteratorChunk - mergedChunks.push_back(iteratorChunk); - ++i; - } - } - - // saved merged chunk vector - (*binIter).second = mergedChunks; - } - } -} - -// 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); - - // create new chunk - Chunk newChunk(saveOffset, lastOffset); - - // if entry doesn't exist - if ( binIter == binMap.end() ) { - ChunkVector newChunks; - newChunks.push_back(newChunk); - binMap.insert( pair(saveBin, newChunks)); - } - - // otherwise - else { - ChunkVector& binChunks = (*binIter).second; - binChunks.push_back( newChunk ); - } -} - -// 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 ) - 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 structs & typedefs - -namespace BamTools { - -// individual index offset entry -struct BamToolsIndexEntry { - - // data members - int32_t MaxEndPosition; - int64_t StartOffset; - int32_t StartPosition; - - // ctor - 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) - { } -}; - -// 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 - 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); - ~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); -}; - -// 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; - - // 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 - 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, storing index entries - BamAlignment 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; - } - - // if beginning of block, save first alignment's refID & position - if ( currentBlockCount == 0 ) { - 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 == 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(); - } - - // 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* 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 - - // 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; - } - - // 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; -} - -// 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; - 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; - } - - // 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 - 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) { - - // 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; - } - - // swap endian-ness if necessary - if ( m_isBigEndian ) { - SwapEndian_32(entry.MaxEndPosition); - SwapEndian_64(entry.StartOffset); - SwapEndian_32(entry.StartPosition); - } - - // 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; - 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/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 = 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 - 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); - } - - // 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(); } diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h index d8447fa..b54aace 100644 --- a/src/api/BamIndex.h +++ b/src/api/BamIndex.h @@ -3,10 +3,9 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 20 October 2010 (DB) +// Last modified: 19 November 2010 (DB) // --------------------------------------------------------------------------- -// Provides index functionality - both for the standardized BAM index format -// (".bai") as well as a BamTools-specific (nonstandard) index format (".bti"). +// Provides basic BAM index interface // *************************************************************************** #ifndef BAM_INDEX_H @@ -22,7 +21,12 @@ namespace BamTools { class BamReader; class BgzfData; - + +namespace Internal { + class BamStandardIndex; + class BamToolsIndex; +} // namespace Internal + // -------------------------------------------------- // BamIndex base class class API_EXPORT BamIndex { @@ -129,180 +133,12 @@ class API_EXPORT BamIndex { BamTools::RefVector m_references; BamIndex::BamIndexCacheMode m_cacheMode; FILE* m_indexStream; -}; - -// -------------------------------------------------- -// BamStandardIndex class -// -// implements standardized (per SAM/BAM spec) index file ops -class BamStandardIndex : public BamIndex { - - // ctor & dtor - public: - BamStandardIndex(BamTools::BgzfData* bgzf, - BamTools::BamReader* reader); - ~BamStandardIndex(void); - - // interface (implements BamIndex virtual methods) - public: - // 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(".bai"); } - // returns whether reference has alignments or no - bool HasAlignments(const int& referenceID) const; - // attempts to use index to jump to region; returns success/fail - // a "successful" jump indicates no error, but not whether this region has data - // * thus, the method sets a flag to indicate whether there are alignments - // available after the jump position - bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); - protected: - // clear all current index offset data in memory - void ClearAllData(void); - // return file position after header metadata - const off_t DataBeginOffset(void) const; - // return true if all index data is cached - bool HasFullDataCache(void) const; - // 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 first reference begin, return true if skipped OK - bool SkipToFirstReference(void); - // write index reference data - bool WriteAllReferences(void); - // write index header data - bool WriteHeader(void); - // internal implementation - private: - struct BamStandardIndexPrivate; - BamStandardIndexPrivate* d; + friend class Internal::BamStandardIndex; + friend class Internal::BamToolsIndex; }; -// -------------------------------------------------- -// BamToolsIndex class -// -// implements BamTools-specific index file ops -class BamToolsIndex : public BamIndex { - - // ctor & dtor - public: - BamToolsIndex(BamTools::BgzfData* bgzf, - BamTools::BamReader* reader); - ~BamToolsIndex(void); - - // interface (implements BamIndex virtual methods) - public: - // 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"); } - // returns whether reference has alignments or no - bool HasAlignments(const int& referenceID) const; - // attempts to use index to jump to region; returns success/fail - // a "successful" jump indicates no error, but not whether this region has data - // * thus, the method sets a flag to indicate whether there are alignments - // available after the jump position - bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); - protected: - // clear all current index offset data in memory - void ClearAllData(void); - // return file position after header metadata - const off_t DataBeginOffset(void) const; - // return true if all index data is cached - bool HasFullDataCache(void) const; - // 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 first reference begin, return true if skipped OK - bool SkipToFirstReference(void); - // write index reference data - bool WriteAllReferences(void); - // write index header data - bool WriteHeader(void); - - // internal implementation - private: - struct BamToolsIndexPrivate; - BamToolsIndexPrivate* d; -}; - -// -------------------------------------------------- -// BamIndex factory methods - -// returns index based on BAM filename 'stub' -// checks first for preferred type, returns that type if found -// (if not found, attmempts to load other type(s), returns 0 if NONE found) -// -// ** default preferred type is BamToolsIndex ** use this anytime it exists -inline -BamIndex* BamIndex::FromBamFilename(const std::string& bamFilename, - BamTools::BgzfData* bgzf, - BamTools::BamReader* reader, - const BamIndex::PreferredIndexType& type) -{ - // --------------------------------------------------- - // attempt to load preferred type first - - const std::string bamtoolsIndexFilename = bamFilename + ".bti"; - const bool bamtoolsIndexExists = BamTools::FileExists(bamtoolsIndexFilename); - if ( (type == BamIndex::BAMTOOLS) && bamtoolsIndexExists ) - return new BamToolsIndex(bgzf, reader); - - const std::string standardIndexFilename = bamFilename + ".bai"; - const bool standardIndexExists = BamTools::FileExists(standardIndexFilename); - if ( (type == BamIndex::STANDARD) && standardIndexExists ) - return new BamStandardIndex(bgzf, reader); - - // ---------------------------------------------------- - // preferred type could not be found, try other (non-preferred) types - // if none found, return 0 - - if ( bamtoolsIndexExists ) return new BamToolsIndex(bgzf, reader); - if ( standardIndexExists ) return new BamStandardIndex(bgzf, reader); - return 0; -} - -// returns index based on explicitly named index file (or 0 if not found) -inline -BamIndex* BamIndex::FromIndexFilename(const std::string& indexFilename, - BamTools::BgzfData* bgzf, - BamTools::BamReader* reader) -{ - // see if specified file exists - const bool indexExists = BamTools::FileExists(indexFilename); - if ( !indexExists ) return 0; - - const std::string bamtoolsIndexExtension(".bti"); - const std::string standardIndexExtension(".bai"); - - // if has bamtoolsIndexExtension - if ( indexFilename.find(bamtoolsIndexExtension) == (indexFilename.length() - bamtoolsIndexExtension.length()) ) - return new BamToolsIndex(bgzf, reader); - - // if has standardIndexExtension - if ( indexFilename.find(standardIndexExtension) == (indexFilename.length() - standardIndexExtension.length()) ) - return new BamStandardIndex(bgzf, reader); - - // otherwise, unsupported file type - return 0; -} - } // namespace BamTools #endif // BAM_INDEX_H diff --git a/src/api/BamReader_p.cpp b/src/api/BamReader_p.cpp index 65a49ed..792be22 100644 --- a/src/api/BamReader_p.cpp +++ b/src/api/BamReader_p.cpp @@ -10,7 +10,10 @@ #include #include +#include +#include #include + using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamStandardIndex.cpp b/src/api/BamStandardIndex.cpp new file mode 100644 index 0000000..28db076 --- /dev/null +++ b/src/api/BamStandardIndex.cpp @@ -0,0 +1,910 @@ +// *************************************************************************** +// BamStandardIndex.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 November 2010 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the standardized BAM index format (".bai") +// *************************************************************************** + +#include +#include +#include +#include +using namespace BamTools; +using namespace BamTools::Internal; + +#include +#include +#include +#include +#include +using namespace std; + +BamStandardIndex::BamStandardIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) + , m_dataBeginOffset(0) + , m_hasFullDataCache(false) +{ + m_isBigEndian = BamTools::SystemIsBigEndian(); +} + +BamStandardIndex::~BamStandardIndex(void) { + ClearAllData(); +} + +// calculate bins that overlap region +int BamStandardIndex::BinsFromRegion(const BamRegion& region, + const bool isRightBoundSpecified, + uint16_t bins[MAX_BIN]) +{ + // get region boundaries + uint32_t begin = (unsigned int)region.LeftPosition; + uint32_t end; + + // if right bound specified AND left&right bounds are on same reference + // OK to use right bound position + if ( isRightBoundSpecified && ( region.LeftRefID == region.RightRefID ) ) + end = (unsigned int)region.RightPosition; + + // otherwise, use end of left bound reference as cutoff + else + end = (unsigned int)m_references.at(region.LeftRefID).RefLength - 1; + + // initialize list, bin '0' always a valid bin + int i = 0; + bins[i++] = 0; + + // get rest of bins that contain this region + unsigned int k; + for (k = 1 + (begin>>26); k <= 1 + (end>>26); ++k) { bins[i++] = k; } + for (k = 9 + (begin>>23); k <= 9 + (end>>23); ++k) { bins[i++] = k; } + for (k = 73 + (begin>>20); k <= 73 + (end>>20); ++k) { bins[i++] = k; } + for (k = 585 + (begin>>17); k <= 585 + (end>>17); ++k) { bins[i++] = k; } + for (k = 4681 + (begin>>14); k <= 4681 + (end>>14); ++k) { bins[i++] = k; } + + // return number of bins stored + return i; +} + +// creates index data (in-memory) from current reader data +bool BamStandardIndex::Build(void) { + + // be sure reader & BGZF file are valid & open for reading + if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen ) + return false; + + // move file pointer to beginning of alignments + m_reader->Rewind(); + + // get reference count, reserve index space + const int numReferences = (int)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; + + // bin data + uint32_t saveBin(defaultValue); + uint32_t lastBin(defaultValue); + + // reference ID data + int32_t saveRefID(defaultValue); + int32_t lastRefID(defaultValue); + + // offset data + uint64_t saveOffset = m_BGZF->Tell(); + uint64_t lastOffset = saveOffset; + + // coordinate data + int32_t lastCoordinate = defaultValue; + + BamAlignment bAlignment; + while ( m_reader->GetNextAlignmentCore(bAlignment) ) { + + // change of chromosome, save ID, reset bin + if ( lastRefID != bAlignment.RefID ) { + lastRefID = bAlignment.RefID; + lastBin = defaultValue; + } + + // if lastCoordinate greater than BAM position - file not sorted properly + else if ( lastCoordinate > bAlignment.Position ) { + 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); + exit(1); + } + + // if valid reference && BAM bin spans some minimum cutoff (smaller bin ids span larger regions) + if ( (bAlignment.RefID >= 0) && (bAlignment.Bin < 4681) ) { + + // save linear offset entry (matched to BAM entry refID) + BamStandardIndexData::iterator indexIter = m_indexData.find(bAlignment.RefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; + LinearOffsetVector& offsets = refIndex.Offsets; + SaveLinearOffset(offsets, bAlignment, lastOffset); + } + + // if current BamAlignment bin != lastBin, "then possibly write the binning index" + if ( bAlignment.Bin != lastBin ) { + + // if not first time through + if ( saveBin != defaultValue ) { + + // save Bam bin entry + BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; + BamBinMap& binMap = refIndex.Bins; + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); + } + + // update saveOffset + saveOffset = lastOffset; + + // update bin values + saveBin = bAlignment.Bin; + lastBin = bAlignment.Bin; + + // update saveRefID + saveRefID = bAlignment.RefID; + + // if invalid RefID, break out + if ( saveRefID < 0 ) break; + } + + // make sure that current file pointer is beyond lastOffset + if ( m_BGZF->Tell() <= (int64_t)lastOffset ) { + fprintf(stderr, "Error in BGZF offsets.\n"); + exit(1); + } + + // update lastOffset + lastOffset = m_BGZF->Tell(); + + // update lastCoordinate + lastCoordinate = bAlignment.Position; + } + + // save any leftover BAM data (as long as refID is valid) + if ( saveRefID >= 0 ) { + // save Bam bin entry + BamStandardIndexData::iterator indexIter = m_indexData.find(saveRefID); + if ( indexIter == m_indexData.end() ) return false; // error + ReferenceIndex& refIndex = (*indexIter).second; + BamBinMap& binMap = refIndex.Bins; + SaveBinEntry(binMap, saveBin, saveOffset, lastOffset); + } + + // simplify index by merging chunks + MergeChunks(); + + // iterate through references in index + // 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).second; + LinearOffsetVector& offsets = refIndex.Offsets; + + // sort linear offsets + sort(offsets.begin(), offsets.end()); + } + + // rewind file pointer to beginning of alignments, return success/fail + return m_reader->Rewind(); +} + +// check index file magic number, return true if OK +bool BamStandardIndex::CheckMagicNumber(void) { + + // read in magic number + char magic[4]; + size_t elementsRead = fread(magic, sizeof(char), 4, m_indexStream); + + // compare to expected value + if ( strncmp(magic, "BAI\1", 4) != 0 ) { + fprintf(stderr, "Problem with index file - invalid format.\n"); + fclose(m_indexStream); + return false; + } + + // return success/failure of load + return (elementsRead == 4); +} + +// clear all current index offset data in memory +void BamStandardIndex::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::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::DataBeginOffset(void) const { + return m_dataBeginOffset; +} + +// calculates offset(s) for a given region +bool BamStandardIndex::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 + 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; + 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 ) { + + const uint16_t binKey = bins[i]; + 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(); + for ( ; chunksIter != chunksEnd; ++chunksIter) { + + // if valid chunk found, store its file offset + const Chunk& chunk = (*chunksIter); + if ( chunk.Stop > minOffset ) + offsets.push_back( chunk.Start ); + } + } + } + + // clean up memory + free(bins); + + // sort the offsets before returning + sort(offsets.begin(), offsets.end()); + + // set flag & return success + *hasAlignmentsInRegion = (offsets.size() != 0 ); + + // if cache mode set to none, dump the data we just loaded + if (m_cacheMode == BamIndex::NoIndexCaching ) + ClearReferenceOffsets(region.LeftRefID); + + // return succes + return true; +} + +// returns whether reference has alignments or no +bool BamStandardIndex::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; +} + +// return true if all index data is cached +bool BamStandardIndex::HasFullDataCache(void) const { + return m_hasFullDataCache; +} + +// returns true if index cache has data for desired reference +bool BamStandardIndex::IsDataLoaded(const int& refId) const { + + // look up refId, return false if not found + BamStandardIndexData::const_iterator indexIter = m_indexData.find(refId); + if ( indexIter == m_indexData.end() ) return false; + + // 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() ); +} + +// attempts to use index to jump to region; returns success/fail +bool BamStandardIndex::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { + + // be sure reader & BGZF file are valid & open for reading + if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen ) + return false; + + // make sure left-bound position is valid + if ( region.LeftPosition > m_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, 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 &= m_BGZF->Seek(*o); + *hasAlignmentsInRegion = m_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 m_BGZF->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::KeepOnlyFirstReferenceOffsets(void) { + BamStandardIndexData::const_iterator indexBegin = m_indexData.begin(); + KeepOnlyReferenceOffsets((*indexBegin).first); +} + +// clears index data from all references except the one specified +void BamStandardIndex::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::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::LoadHeader(void) { + + bool loadedOk = CheckMagicNumber(); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(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::LoadBin(ReferenceIndex& refEntry, bool saveData) { + + size_t elementsRead = 0; + + // get bin ID + uint32_t binId; + elementsRead += fread(&binId, sizeof(binId), 1, 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::LoadBins(ReferenceIndex& refEntry, bool saveData) { + + size_t elementsRead = 0; + + // get number of bins + int32_t numBins; + elementsRead += fread(&numBins, sizeof(numBins), 1, 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::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_indexStream); + elementsRead += fread(&stop, sizeof(stop), 1, m_indexStream); + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_64(start); + SwapEndian_64(stop); + } + + // save data if requested + if ( saveData ) chunks.push_back( Chunk(start, stop) ); + + // return success/failure of load + return ( elementsRead == 2 ); +} + +bool BamStandardIndex::LoadChunks(ChunkVector& chunks, bool saveData) { + + size_t elementsRead = 0; + + // read in number of chunks + uint32_t numChunks; + elementsRead += fread(&numChunks, sizeof(numChunks), 1, 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::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_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_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::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::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::LoadReferenceCount(int& numReferences) { + + size_t elementsRead = 0; + + // read reference count + elementsRead += fread(&numReferences, sizeof(numReferences), 1, 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 BamStandardIndex::MergeChunks(void) { + + // iterate over reference enties + 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).second; + BamBinMap& bamBinMap = refIndex.Bins; + + // iterate over BAM bins + BamBinMap::iterator binIter = bamBinMap.begin(); + BamBinMap::iterator binEnd = bamBinMap.end(); + for ( ; binIter != binEnd; ++binIter ) { + + // get chunk vector for this bin + ChunkVector& binChunks = (*binIter).second; + if ( binChunks.size() == 0 ) continue; + + ChunkVector mergedChunks; + mergedChunks.push_back( binChunks[0] ); + + // iterate over chunks + int i = 0; + ChunkVector::iterator chunkIter = binChunks.begin(); + ChunkVector::iterator chunkEnd = binChunks.end(); + for ( ++chunkIter; chunkIter != chunkEnd; ++chunkIter) { + + // get 'currentChunk' based on numeric index + Chunk& currentChunk = mergedChunks[i]; + + // get iteratorChunk based on vector iterator + Chunk& iteratorChunk = (*chunkIter); + + // if chunk ends where (iterator) chunk starts, then merge + if ( currentChunk.Stop>>16 == iteratorChunk.Start>>16 ) + currentChunk.Stop = iteratorChunk.Stop; + + // otherwise + else { + // set currentChunk + 1 to iteratorChunk + mergedChunks.push_back(iteratorChunk); + ++i; + } + } + + // saved merged chunk vector + (*binIter).second = mergedChunks; + } + } +} + +// saves BAM bin entry for index +void BamStandardIndex::SaveBinEntry(BamBinMap& binMap, + const uint32_t& saveBin, + const uint64_t& saveOffset, + const uint64_t& lastOffset) +{ + // look up saveBin + BamBinMap::iterator binIter = binMap.find(saveBin); + + // create new chunk + Chunk newChunk(saveOffset, lastOffset); + + // if entry doesn't exist + if ( binIter == binMap.end() ) { + ChunkVector newChunks; + newChunks.push_back(newChunk); + binMap.insert( pair(saveBin, newChunks)); + } + + // otherwise + else { + ChunkVector& binChunks = (*binIter).second; + binChunks.push_back( newChunk ); + } +} + +// saves linear offset entry for index +void BamStandardIndex::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::SetReferenceCount(const int& count) { + for ( int i = 0; i < count; ++i ) + m_indexData[i].HasAlignments = false; +} + +bool BamStandardIndex::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::SkipToReference(const int& refId) { + + // attempt rewind + if ( !Rewind() ) return false; + + // read in number of references + uint32_t numReferences; + size_t elementsRead = fread(&numReferences, sizeof(numReferences), 1, 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::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write magic number + elementsWritten += fwrite("BAI\1", sizeof(char), 4, m_indexStream); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_indexStream); + + // return success/failure of write + return (elementsWritten == 4); +} + +// write index data for all references to new index file +bool BamStandardIndex::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_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::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_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::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_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::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_indexStream); + elementsWritten += fwrite(&stop, sizeof(stop), 1, m_indexStream); + + // return success/failure of write + return ( elementsWritten == 2 ); +} + +// write index data for chunk entry to new index file +bool BamStandardIndex::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_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::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_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_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::WriteReference(const ReferenceIndex& refEntry) { + bool refOk = true; + refOk &= WriteBins(refEntry.Bins); + refOk &= WriteLinearOffsets(refEntry.Offsets); + return refOk; +} diff --git a/src/api/BamStandardIndex.h b/src/api/BamStandardIndex.h new file mode 100644 index 0000000..da179f4 --- /dev/null +++ b/src/api/BamStandardIndex.h @@ -0,0 +1,213 @@ +// *************************************************************************** +// BamStandardIndex.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 November 2010 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the standardized BAM index format (".bai") +// *************************************************************************** + +#ifndef BAM_STANDARD_INDEX_FORMAT_H +#define BAM_STANDARD_INDEX_FORMAT_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to +// version without notice, or even be removed. +// +// We mean it. + +#include +#include +#include +#include +#include + +namespace BamTools { + +class BamAlignment; + +namespace Internal { + +// 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 { + + // data members + uint64_t Start; + uint64_t Stop; + + // constructor + Chunk(const uint64_t& start = 0, + const uint64_t& stop = 0) + : Start(start) + , Stop(stop) + { } +}; + +inline +bool ChunkLessThan(const Chunk& lhs, const Chunk& rhs) { + return lhs.Start < rhs.Start; +} + +typedef std::vector ChunkVector; +typedef std::map BamBinMap; +typedef std::vector LinearOffsetVector; + +struct ReferenceIndex { + + // data members + BamBinMap Bins; + LinearOffsetVector Offsets; + bool HasAlignments; + + // constructor + ReferenceIndex(const BamBinMap& binMap = BamBinMap(), + const LinearOffsetVector& offsets = LinearOffsetVector(), + const bool hasAlignments = false) + : Bins(binMap) + , Offsets(offsets) + , HasAlignments(hasAlignments) + { } +}; + +typedef std::map BamStandardIndexData; + +class BamStandardIndex : public BamIndex { + + // ctor & dtor + public: + BamStandardIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader); + ~BamStandardIndex(void); + + // interface (implements BamIndex virtual methods) + public: + // 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(".bai"); } + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // attempts to use index to jump to region; returns success/fail + // a "successful" jump indicates no error, but not whether this region has data + // * thus, the method sets a flag to indicate whether there are alignments + // available after the jump position + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + public: + // clear all current index offset data in memory + void ClearAllData(void); + // return file position after header metadata + const off_t DataBeginOffset(void) const; + // return true if all index data is cached + bool HasFullDataCache(void) const; + // 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 first reference begin, return true if skipped OK + bool SkipToFirstReference(void); + // write index reference data + bool WriteAllReferences(void); + // write index header data + bool WriteHeader(void); + + // 'internal' methods + public: + + // ----------------------- + // 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[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, + std::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); + + // data members + private: + + BamStandardIndexData m_indexData; + off_t m_dataBeginOffset; + bool m_hasFullDataCache; + bool m_isBigEndian; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAM_STANDARD_INDEX_FORMAT_H diff --git a/src/api/BamToolsIndex.cpp b/src/api/BamToolsIndex.cpp new file mode 100644 index 0000000..3bb314b --- /dev/null +++ b/src/api/BamToolsIndex.cpp @@ -0,0 +1,577 @@ +// *************************************************************************** +// BamToolsIndex.cpp (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 November 2010 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the BamTools index format (".bti") +// *************************************************************************** + +#include +#include +#include +#include +using namespace BamTools; +using namespace BamTools::Internal; + +#include +#include +#include +#include +#include +using namespace std; + +BamToolsIndex::BamToolsIndex(BgzfData* bgzf, BamReader* reader) + : BamIndex(bgzf, reader) + , 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::~BamToolsIndex(void) { + ClearAllData(); +} + +// creates index data (in-memory) from current reader data +bool BamToolsIndex::Build(void) { + + // be sure reader & BGZF file are valid & open for reading + if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen ) + return false; + + // move file pointer to beginning of alignments + if ( !m_reader->Rewind() ) return false; + + // initialize index data structure with space for all references + const int numReferences = (int)m_references.size(); + m_indexData.clear(); + m_hasFullDataCache = false; + SetReferenceCount(numReferences); + + // set up counters and markers + int32_t currentBlockCount = 0; + int64_t currentAlignmentOffset = m_BGZF->Tell(); + int32_t blockRefId = 0; + int32_t blockMaxEndPosition = 0; + int64_t blockStartOffset = currentAlignmentOffset; + int32_t blockStartPosition = -1; + + // plow through alignments, storing index entries + BamAlignment al; + while ( m_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; + } + + // if beginning of block, save first alignment's refID & position + if ( currentBlockCount == 0 ) { + 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 == m_blockSize ) { + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); + blockStartOffset = m_BGZF->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 = m_BGZF->Tell(); + } + + // store final block with data + BamToolsIndexEntry entry(blockMaxEndPosition, blockStartOffset, blockStartPosition); + SaveOffsetEntry(blockRefId, entry); + + // set flag + m_hasFullDataCache = true; + + // return success/failure of rewind + return m_reader->Rewind(); +} + +// check index file magic number, return true if OK +bool BamToolsIndex::CheckMagicNumber(void) { + + // see if index is valid BAM index + char magic[4]; + size_t elementsRead = fread(magic, 1, 4, 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::CheckVersion(void) { + + // read version from file + size_t elementsRead = fread(&m_inputVersion, sizeof(m_inputVersion), 1, 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::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::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::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::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 + + // 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; + } + + // 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_cacheMode == BamIndex::NoIndexCaching ) + ClearReferenceOffsets(region.LeftRefID); + + // return success + return true; +} + +// returns whether reference has alignments or no +bool BamToolsIndex::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::HasFullDataCache(void) const { + return m_hasFullDataCache; +} + +// returns true if index cache has data for desired reference +bool BamToolsIndex::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::Jump(const BamRegion& region, bool* hasAlignmentsInRegion) { + + // clear flag + *hasAlignmentsInRegion = false; + + // check valid BamReader state + if ( m_reader == 0 || m_BGZF == 0 || !m_reader->IsOpen() ) { + fprintf(stderr, "ERROR: Could not jump: invalid BamReader state.\n"); + return false; + } + + // make sure left-bound position is valid + if ( region.LeftPosition > m_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 m_BGZF->Seek(offset); +} + +// clears index data from all references except the first +void BamToolsIndex::KeepOnlyFirstReferenceOffsets(void) { + BamToolsIndexData::const_iterator indexBegin = m_indexData.begin(); + KeepOnlyReferenceOffsets( (*indexBegin).first ); +} + +// clears index data from all references except the one specified +void BamToolsIndex::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::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::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_indexStream); + if ( elementsRead != 1 ) return false; + if ( m_isBigEndian ) SwapEndian_32(m_blockSize); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(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::LoadIndexEntry(const int& refId, bool saveData) { + + // read in index entry data members + size_t elementsRead = 0; + BamToolsIndexEntry entry; + elementsRead += fread(&entry.MaxEndPosition, sizeof(entry.MaxEndPosition), 1, m_indexStream); + elementsRead += fread(&entry.StartOffset, sizeof(entry.StartOffset), 1, m_indexStream); + elementsRead += fread(&entry.StartPosition, sizeof(entry.StartPosition), 1, m_indexStream); + if ( elementsRead != 3 ) { + cerr << "Error reading index entry. Expected 3 elements, read in: " << elementsRead << endl; + return false; + } + + // swap endian-ness if necessary + if ( m_isBigEndian ) { + SwapEndian_32(entry.MaxEndPosition); + SwapEndian_64(entry.StartOffset); + SwapEndian_32(entry.StartPosition); + } + + // 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::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::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_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::LoadReferenceCount(int& numReferences) { + + size_t elementsRead = 0; + + // read reference count + elementsRead += fread(&numReferences, sizeof(numReferences), 1, 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::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::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::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::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::SkipToReference(const int& refId) { + + // attempt rewind + if ( !Rewind() ) return false; + + // read in number of references + int32_t numReferences; + size_t elementsRead = fread(&numReferences, sizeof(numReferences), 1, 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/failure of skip + return skippedOk; +} + +// write header to new index file +bool BamToolsIndex::WriteHeader(void) { + + size_t elementsWritten = 0; + + // write BTI index format 'magic number' + elementsWritten += fwrite("BTI\1", 1, 4, 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_indexStream); + + // write block size + int32_t blockSize = m_blockSize; + if ( m_isBigEndian ) SwapEndian_32(blockSize); + elementsWritten += fwrite(&blockSize, sizeof(blockSize), 1, m_indexStream); + + // store offset of beginning of data + m_dataBeginOffset = ftell64(m_indexStream); + + // return success/failure of write + return ( elementsWritten == 6 ); +} + +// write index data for all references to new index file +bool BamToolsIndex::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_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::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_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::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); + } + + // write the reference index entry + size_t elementsWritten = 0; + elementsWritten += fwrite(&maxEndPosition, sizeof(maxEndPosition), 1, m_indexStream); + elementsWritten += fwrite(&startOffset, sizeof(startOffset), 1, m_indexStream); + elementsWritten += fwrite(&startPosition, sizeof(startPosition), 1, m_indexStream); + return ( elementsWritten == 3 ); +} diff --git a/src/api/BamToolsIndex.h b/src/api/BamToolsIndex.h new file mode 100644 index 0000000..c99834d --- /dev/null +++ b/src/api/BamToolsIndex.h @@ -0,0 +1,192 @@ +// *************************************************************************** +// BamToolsIndex.h (c) 2010 Derek Barnett +// Marth Lab, Department of Biology, Boston College +// All rights reserved. +// --------------------------------------------------------------------------- +// Last modified: 19 November 2010 (DB) +// --------------------------------------------------------------------------- +// Provides index operations for the BamTools index format (".bti") +// *************************************************************************** + +#ifndef BAMTOOLS_INDEX_FORMAT_H +#define BAMTOOLS_INDEX_FORMAT_H + +// ------------- +// W A R N I N G +// ------------- +// +// This file is not part of the BamTools API. It exists purely as an +// implementation detail. This header file may change from version to +// version without notice, or even be removed. +// +// We mean it. + +#include +#include +#include +#include +#include + +namespace BamTools { + +namespace Internal { + +// individual index offset entry +struct BamToolsIndexEntry { + + // data members + int32_t MaxEndPosition; + int64_t StartOffset; + int32_t StartPosition; + + // ctor + 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; + std::vector Offsets; + + // ctor + BamToolsReferenceEntry(void) + : HasAlignments(false) + { } +}; + +// the actual index data structure +typedef std::map BamToolsIndexData; + +class BamToolsIndex : public BamIndex { + + // 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 + }; + + + // ctor & dtor + public: + BamToolsIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader); + ~BamToolsIndex(void); + + // interface (implements BamIndex virtual methods) + public: + // 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"); } + // returns whether reference has alignments or no + bool HasAlignments(const int& referenceID) const; + // attempts to use index to jump to region; returns success/fail + // a "successful" jump indicates no error, but not whether this region has data + // * thus, the method sets a flag to indicate whether there are alignments + // available after the jump position + bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion); + public: + // clear all current index offset data in memory + void ClearAllData(void); + // return file position after header metadata + const off_t DataBeginOffset(void) const; + // return true if all index data is cached + bool HasFullDataCache(void) const; + // 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 first reference begin, return true if skipped OK + bool SkipToFirstReference(void); + // write index reference data + bool WriteAllReferences(void); + // write index header data + bool WriteHeader(void); + + // 'internal' methods + public: + + // ----------------------- + // 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); + + // data members + private: + 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; +}; + +} // namespace Internal +} // namespace BamTools + +#endif // BAMTOOLS_INDEX_FORMAT_H diff --git a/src/api/BamWriter_p.cpp b/src/api/BamWriter_p.cpp index ca9f76a..9887d56 100644 --- a/src/api/BamWriter_p.cpp +++ b/src/api/BamWriter_p.cpp @@ -15,7 +15,7 @@ using namespace BamTools::Internal; using namespace std; BamWriterPrivate::BamWriterPrivate(void) { - IsBigEndian = SystemIsBigEndian(); + IsBigEndian = SystemIsBigEndian(); } BamWriterPrivate::~BamWriterPrivate(void) { diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 092254b..7c1b8ff 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -18,6 +18,8 @@ add_library ( BamTools SHARED BamMultiReader.cpp BamReader.cpp BamReader_p.cpp + BamStandardIndex.cpp + BamToolsIndex.cpp BamWriter.cpp BamWriter_p.cpp BGZF.cpp -- 2.39.2