#include <api/BamIndex.h>
#include <api/BamReader.h>
#include <api/BGZF.h>
+#include <api/BamStandardIndex.h>
+#include <api/BamToolsIndex.h>
using namespace BamTools;
+using namespace BamTools::Internal;
#include <cstdio>
#include <cstdlib>
#include <map>
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
// 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<Chunk> ChunkVector;
-typedef map<uint32_t, ChunkVector> BamBinMap;
-typedef vector<uint64_t> 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<int32_t, ReferenceIndex> 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<int64_t>& 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<int64_t>& 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<uint32_t, ChunkVector>::const_iterator binIter = binMap.find(binKey);
- if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) {
-
- // iterate over chunks
- const ChunkVector& chunks = (*binIter).second;
- std::vector<Chunk>::const_iterator chunksIter = chunks.begin();
- std::vector<Chunk>::const_iterator chunksEnd = chunks.end();
- for ( ; chunksIter != chunksEnd; ++chunksIter) {
-
- // if valid chunk found, store its file offset
- const Chunk& chunk = (*chunksIter);
- if ( chunk.Stop > minOffset )
- offsets.push_back( chunk.Start );
- }
- }
- }
-
- // clean up memory
- free(bins);
-
- // sort the offsets before returning
- sort(offsets.begin(), offsets.end());
-
- // 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<int64_t> 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<int64_t>::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<uint32_t, ChunkVector>(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<int32_t, ReferenceIndex>(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<uint32_t, ChunkVector>(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<BamToolsIndexEntry> Offsets;
-
- // ctor
- BamToolsReferenceEntry(void)
- : HasAlignments(false)
- { }
-};
-
-// the actual index data structure
-typedef map<int, BamToolsReferenceEntry> 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<BamToolsIndexEntry>& 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<BamToolsIndexEntry>& 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<BamToolsIndexEntry>::const_iterator offsetIter = referenceOffsets.begin();
- vector<BamToolsIndexEntry>::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<BamToolsIndexEntry>::const_iterator offsetIter = refEntry.Offsets.begin();
- vector<BamToolsIndexEntry>::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(); }
// 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
class BamReader;
class BgzfData;
-
+
+namespace Internal {
+ class BamStandardIndex;
+ class BamToolsIndex;
+} // namespace Internal
+
// --------------------------------------------------
// BamIndex base class
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
#include <api/BamReader.h>
#include <api/BamReader_p.h>
+#include <api/BamStandardIndex.h>
+#include <api/BamToolsIndex.h>
#include <api/BGZF.h>
+
using namespace BamTools;
using namespace BamTools::Internal;
--- /dev/null
+// ***************************************************************************
+// 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 <api/BamAlignment.h>
+#include <api/BamReader.h>
+#include <api/BamStandardIndex.h>
+#include <api/BGZF.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+#include <cstdlib>
+#include <algorithm>
+#include <iostream>
+#include <map>
+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<int64_t>& 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<uint32_t, ChunkVector>::const_iterator binIter = binMap.find(binKey);
+ if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) {
+
+ // iterate over chunks
+ const ChunkVector& chunks = (*binIter).second;
+ std::vector<Chunk>::const_iterator chunksIter = chunks.begin();
+ std::vector<Chunk>::const_iterator chunksEnd = chunks.end();
+ for ( ; chunksIter != chunksEnd; ++chunksIter) {
+
+ // if valid chunk found, store its file offset
+ const Chunk& chunk = (*chunksIter);
+ if ( chunk.Stop > minOffset )
+ offsets.push_back( chunk.Start );
+ }
+ }
+ }
+
+ // clean up memory
+ free(bins);
+
+ // sort the offsets before returning
+ sort(offsets.begin(), offsets.end());
+
+ // 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<int64_t> 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<int64_t>::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<uint32_t, ChunkVector>(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<int32_t, ReferenceIndex>(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<uint32_t, ChunkVector>(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;
+}
--- /dev/null
+// ***************************************************************************
+// 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 <api/BamAux.h>
+#include <api/BamIndex.h>
+#include <map>
+#include <string>
+#include <vector>
+
+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<Chunk> ChunkVector;
+typedef std::map<uint32_t, ChunkVector> BamBinMap;
+typedef std::vector<uint64_t> 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<int32_t, ReferenceIndex> 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<int64_t>& 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
--- /dev/null
+// ***************************************************************************
+// 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 <api/BamAlignment.h>
+#include <api/BamReader.h>
+#include <api/BamToolsIndex.h>
+#include <api/BGZF.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+#include <cstdlib>
+#include <algorithm>
+#include <iostream>
+#include <map>
+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<BamToolsIndexEntry>& 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<BamToolsIndexEntry>& 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<BamToolsIndexEntry>::const_iterator offsetIter = referenceOffsets.begin();
+ vector<BamToolsIndexEntry>::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<BamToolsIndexEntry>::const_iterator offsetIter = refEntry.Offsets.begin();
+ vector<BamToolsIndexEntry>::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 );
+}
--- /dev/null
+// ***************************************************************************
+// 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 <api/BamAux.h>
+#include <api/BamIndex.h>
+#include <map>
+#include <string>
+#include <vector>
+
+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<BamToolsIndexEntry> Offsets;
+
+ // ctor
+ BamToolsReferenceEntry(void)
+ : HasAlignments(false)
+ { }
+};
+
+// the actual index data structure
+typedef std::map<int, BamToolsReferenceEntry> 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
using namespace std;
BamWriterPrivate::BamWriterPrivate(void) {
- IsBigEndian = SystemIsBigEndian();
+ IsBigEndian = SystemIsBigEndian();
}
BamWriterPrivate::~BamWriterPrivate(void) {
BamMultiReader.cpp
BamReader.cpp
BamReader_p.cpp
+ BamStandardIndex.cpp
+ BamToolsIndex.cpp
BamWriter.cpp
BamWriter_p.cpp
BGZF.cpp
projects / bamtools.git / commitdiff