diff spp/src/BamToolsIndex_p.cpp @ 6:ce08b0efa3fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamToolsIndex_p.cpp	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,577 @@
+// ***************************************************************************
+// BamToolsIndex.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 22 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides index operations for the BamTools index format (".bti")
+// ***************************************************************************
+
+#include <BamAlignment.h>
+#include <BamReader.h>
+#include <BGZF.h>
+#include <BamToolsIndex_p.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(&currentVersion, 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 );
+}