+++ /dev/null
-// ***************************************************************************
-// BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 September 2010 (DB)
-// ---------------------------------------------------------------------------
-// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
-// Institute.
-// ---------------------------------------------------------------------------
-// Functionality for simultaneously reading multiple BAM files.
-//
-// This functionality allows applications to work on very large sets of files
-// without requiring intermediate merge, sort, and index steps for each file
-// subset. It also improves the performance of our merge system as it
-// precludes the need to sort merged files.
-// ***************************************************************************
-
-#include <algorithm>
-#include <fstream>
-#include <iostream>
-#include <iterator>
-#include <sstream>
-#include <string>
-#include <vector>
-#include "BGZF.h"
-#include "BamMultiReader.h"
-using namespace BamTools;
-using namespace std;
-
-// -----------------------------------------------------
-// BamMultiReader implementation
-// -----------------------------------------------------
-
-// constructor
-BamMultiReader::BamMultiReader(void)
- : CurrentRefID(0)
- , CurrentLeft(0)
-{ }
-
-// destructor
-BamMultiReader::~BamMultiReader(void) {
- Close();
-}
-
-// close the BAM files
-void BamMultiReader::Close(void) {
-
- // close all BAM readers and clean up pointers
- vector<pair<BamReader*, BamAlignment*> >::iterator readerIter = readers.begin();
- vector<pair<BamReader*, BamAlignment*> >::iterator readerEnd = readers.end();
- for ( ; readerIter != readerEnd; ++readerIter) {
-
- BamReader* reader = (*readerIter).first;
- BamAlignment* alignment = (*readerIter).second;
-
- // close the reader
- if ( reader) reader->Close();
-
- // delete reader pointer
- delete reader;
- reader = 0;
-
- // delete alignment pointer
- delete alignment;
- alignment = 0;
- }
-
- // clear out the container
- readers.clear();
-}
-
-// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
-bool BamMultiReader::CreateIndexes(bool useStandardIndex) {
- bool result = true;
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- result &= reader->CreateIndex(useStandardIndex);
- }
- return result;
-}
-
-// for debugging
-void BamMultiReader::DumpAlignmentIndex(void) {
- for (AlignmentIndex::const_iterator it = alignments.begin(); it != alignments.end(); ++it) {
- cerr << it->first.first << ":" << it->first.second << " " << it->second.first->GetFilename() << endl;
- }
-}
-
-// makes a virtual, unified header for all the bam files in the multireader
-const string BamMultiReader::GetHeaderText(void) const {
-
- string mergedHeader = "";
- map<string, bool> readGroups;
-
- // foreach extraction entry (each BAM file)
- for (vector<pair<BamReader*, BamAlignment*> >::const_iterator rs = readers.begin(); rs != readers.end(); ++rs) {
-
- BamReader* reader = rs->first;
- const string headerText = reader->GetHeaderText();
- if ( headerText.empty() ) continue;
-
- map<string, bool> currentFileReadGroups;
- stringstream header(headerText);
- vector<string> lines;
- string item;
- while (getline(header, item))
- lines.push_back(item);
-
- for (vector<string>::const_iterator it = lines.begin(); it != lines.end(); ++it) {
-
- // get next line from header, skip if empty
- string headerLine = *it;
- if ( headerLine.empty() ) { continue; }
-
- // if first file, save HD & SQ entries
- if ( rs == readers.begin() ) {
- if ( headerLine.find("@HD") == 0 || headerLine.find("@SQ") == 0) {
- mergedHeader.append(headerLine.c_str());
- mergedHeader.append(1, '\n');
- }
- }
-
- // (for all files) append RG entries if they are unique
- if ( headerLine.find("@RG") == 0 ) {
- stringstream headerLineSs(headerLine);
- string part, readGroupPart, readGroup;
- while(std::getline(headerLineSs, part, '\t')) {
- stringstream partSs(part);
- string subtag;
- std::getline(partSs, subtag, ':');
- if (subtag == "ID") {
- std::getline(partSs, readGroup, ':');
- break;
- }
- }
- if (readGroups.find(readGroup) == readGroups.end()) { // prevents duplicate @RG entries
- mergedHeader.append(headerLine.c_str() );
- mergedHeader.append(1, '\n');
- readGroups[readGroup] = true;
- currentFileReadGroups[readGroup] = true;
- } else {
- // warn iff we are reading one file and discover duplicated @RG tags in the header
- // otherwise, we emit no warning, as we might be merging multiple BAM files with identical @RG tags
- if (currentFileReadGroups.find(readGroup) != currentFileReadGroups.end()) {
- cerr << "WARNING: duplicate @RG tag " << readGroup
- << " entry in header of " << reader->GetFilename() << endl;
- }
- }
- }
- }
- }
-
- // return merged header text
- return mergedHeader;
-}
-
-// get next alignment among all files
-bool BamMultiReader::GetNextAlignment(BamAlignment& nextAlignment) {
-
- // bail out if we are at EOF in all files, means no more alignments to process
- if (!HasOpenReaders())
- return false;
-
- // when all alignments have stepped into a new target sequence, update our
- // current reference sequence id
- UpdateReferenceID();
-
- // our lowest alignment and reader will be at the front of our alignment index
- BamAlignment* alignment = alignments.begin()->second.second;
- BamReader* reader = alignments.begin()->second.first;
-
- // now that we have the lowest alignment in the set, save it by copy to our argument
- nextAlignment = BamAlignment(*alignment);
-
- // remove this alignment index entry from our alignment index
- alignments.erase(alignments.begin());
-
- // and add another entry if we can get another alignment from the reader
- if (reader->GetNextAlignment(*alignment)) {
- alignments.insert(make_pair(make_pair(alignment->RefID, alignment->Position),
- make_pair(reader, alignment)));
- } else { // do nothing
- //cerr << "reached end of file " << lowestReader->GetFilename() << endl;
- }
-
- return true;
-
-}
-
-// get next alignment among all files without parsing character data from alignments
-bool BamMultiReader::GetNextAlignmentCore(BamAlignment& nextAlignment) {
-
- // bail out if we are at EOF in all files, means no more alignments to process
- if (!HasOpenReaders())
- return false;
-
- // when all alignments have stepped into a new target sequence, update our
- // current reference sequence id
- UpdateReferenceID();
-
- // our lowest alignment and reader will be at the front of our alignment index
- BamAlignment* alignment = alignments.begin()->second.second;
- BamReader* reader = alignments.begin()->second.first;
-
- // now that we have the lowest alignment in the set, save it by copy to our argument
- nextAlignment = BamAlignment(*alignment);
- //memcpy(&nextAlignment, alignment, sizeof(BamAlignment));
-
- // remove this alignment index entry from our alignment index
- alignments.erase(alignments.begin());
-
- // and add another entry if we can get another alignment from the reader
- if (reader->GetNextAlignmentCore(*alignment)) {
- alignments.insert(make_pair(make_pair(alignment->RefID, alignment->Position),
- make_pair(reader, alignment)));
- } else { // do nothing
- //cerr << "reached end of file " << lowestReader->GetFilename() << endl;
- }
-
- return true;
-
-}
-
-// ---------------------------------------------------------------------------------------
-//
-// NB: The following GetReferenceX() functions assume that we have identical
-// references for all BAM files. We enforce this by invoking the above
-// validation function (ValidateReaders) to verify that our reference data
-// is the same across all files on Open, so we will not encounter a situation
-// in which there is a mismatch and we are still live.
-//
-// ---------------------------------------------------------------------------------------
-
-// returns the number of reference sequences
-const int BamMultiReader::GetReferenceCount(void) const {
- return readers.front().first->GetReferenceCount();
-}
-
-// returns vector of reference objects
-const BamTools::RefVector BamMultiReader::GetReferenceData(void) const {
- return readers.front().first->GetReferenceData();
-}
-
-// returns refID from reference name
-const int BamMultiReader::GetReferenceID(const string& refName) const {
- return readers.front().first->GetReferenceID(refName);
-}
-
-// ---------------------------------------------------------------------------------------
-
-// checks if any readers still have alignments
-bool BamMultiReader::HasOpenReaders() {
- return alignments.size() > 0;
-}
-
-// returns whether underlying BAM readers ALL have an index loaded
-// this is useful to indicate whether Jump() or SetRegion() are possible
-bool BamMultiReader::IsIndexLoaded(void) const {
- bool ok = true;
- vector<pair<BamReader*, BamAlignment*> >::const_iterator readerIter = readers.begin();
- vector<pair<BamReader*, BamAlignment*> >::const_iterator readerEnd = readers.end();
- for ( ; readerIter != readerEnd; ++readerIter ) {
- const BamReader* reader = (*readerIter).first;
- if ( reader ) ok &= reader->IsIndexLoaded();
- }
- return ok;
-}
-
-// jumps to specified region(refID, leftBound) in BAM files, returns success/fail
-bool BamMultiReader::Jump(int refID, int position) {
-
- //if ( References.at(refID).RefHasAlignments && (position <= References.at(refID).RefLength) ) {
- CurrentRefID = refID;
- CurrentLeft = position;
-
- bool result = true;
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- result &= reader->Jump(refID, position);
- if (!result) {
- cerr << "ERROR: could not jump " << reader->GetFilename() << " to " << refID << ":" << position << endl;
- exit(1);
- }
- }
- if (result) UpdateAlignments();
- return result;
-}
-
-// opens BAM files
-bool BamMultiReader::Open(const vector<string>& filenames, bool openIndexes, bool coreMode, bool useDefaultIndex) {
-
- // for filename in filenames
- fileNames = filenames; // save filenames in our multireader
- for (vector<string>::const_iterator it = filenames.begin(); it != filenames.end(); ++it) {
-
- const string filename = *it;
- BamReader* reader = new BamReader;
-
- bool openedOK = true;
- if (openIndexes) {
-
- // leave index filename empty
- // this allows BamReader & BamIndex to search for any available
- // useDefaultIndex gives hint to prefer BAI over BTI
- openedOK = reader->Open(filename, "", true, useDefaultIndex);
- }
-
- // ignoring index file(s)
- else openedOK = reader->Open(filename);
-
- // if file opened ok, check that it can be read
- if ( openedOK ) {
-
- bool fileOK = true;
- BamAlignment* alignment = new BamAlignment;
- fileOK &= ( coreMode ? reader->GetNextAlignmentCore(*alignment) : reader->GetNextAlignment(*alignment) );
-
- if (fileOK) {
- readers.push_back(make_pair(reader, alignment)); // store pointers to our readers for cleanup
- alignments.insert(make_pair(make_pair(alignment->RefID, alignment->Position),
- make_pair(reader, alignment)));
- } else {
- cerr << "WARNING: could not read first alignment in " << filename << ", ignoring file" << endl;
- // if only file available & could not be read, return failure
- if ( filenames.size() == 1 ) return false;
- }
- }
-
- // TODO; any further error handling when openedOK is false ??
- else
- return false;
- }
-
- // files opened ok, at least one alignment could be read,
- // now need to check that all files use same reference data
- ValidateReaders();
- return true;
-}
-
-void BamMultiReader::PrintFilenames(void) {
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- cout << reader->GetFilename() << endl;
- }
-}
-
-// returns BAM file pointers to beginning of alignment data
-bool BamMultiReader::Rewind(void) {
- bool result = true;
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- result &= reader->Rewind();
- }
- return result;
-}
-
-bool BamMultiReader::SetRegion(const int& leftRefID, const int& leftPosition, const int& rightRefID, const int& rightPosition) {
- BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition);
- return SetRegion(region);
-}
-
-bool BamMultiReader::SetRegion(const BamRegion& region) {
-
- Region = region;
-
- // NB: While it may make sense to track readers in which we can
- // successfully SetRegion, In practice a failure of SetRegion means "no
- // alignments here." It makes sense to simply accept the failure,
- // UpdateAlignments(), and continue.
-
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- if (!it->first->SetRegion(region)) {
- cerr << "ERROR: could not jump " << it->first->GetFilename() << " to "
- << region.LeftRefID << ":" << region.LeftPosition
- << ".." << region.RightRefID << ":" << region.RightPosition << endl;
- }
- }
-
- UpdateAlignments();
- return true;
-}
-
-void BamMultiReader::UpdateAlignments(void) {
- // Update Alignments
- alignments.clear();
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* br = it->first;
- BamAlignment* ba = it->second;
- if (br->GetNextAlignment(*ba)) {
- alignments.insert(make_pair(make_pair(ba->RefID, ba->Position),
- make_pair(br, ba)));
- } else {
- // assume BamReader end of region / EOF
- }
- }
-}
-
-// updates the reference id stored in the BamMultiReader
-// to reflect the current state of the readers
-void BamMultiReader::UpdateReferenceID(void) {
- // the alignments are sorted by position, so the first alignment will always have the lowest reference ID
- if (alignments.begin()->second.second->RefID != CurrentRefID) {
- // get the next reference id
- // while there aren't any readers at the next ref id
- // increment the ref id
- int nextRefID = CurrentRefID;
- while (alignments.begin()->second.second->RefID != nextRefID) {
- ++nextRefID;
- }
- //cerr << "updating reference id from " << CurrentRefID << " to " << nextRefID << endl;
- CurrentRefID = nextRefID;
- }
-}
-
-// ValidateReaders checks that all the readers point to BAM files representing
-// alignments against the same set of reference sequences, and that the
-// sequences are identically ordered. If these checks fail the operation of
-// the multireader is undefined, so we force program exit.
-void BamMultiReader::ValidateReaders(void) const {
- int firstRefCount = readers.front().first->GetReferenceCount();
- BamTools::RefVector firstRefData = readers.front().first->GetReferenceData();
- for (vector<pair<BamReader*, BamAlignment*> >::const_iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- BamTools::RefVector currentRefData = reader->GetReferenceData();
- BamTools::RefVector::const_iterator f = firstRefData.begin();
- BamTools::RefVector::const_iterator c = currentRefData.begin();
- if (reader->GetReferenceCount() != firstRefCount || firstRefData.size() != currentRefData.size()) {
- cerr << "ERROR: mismatched number of references in " << reader->GetFilename()
- << " expected " << firstRefCount
- << " reference sequences but only found " << reader->GetReferenceCount() << endl;
- exit(1);
- }
- // this will be ok; we just checked above that we have identically-sized sets of references
- // here we simply check if they are all, in fact, equal in content
- while (f != firstRefData.end()) {
- if (f->RefName != c->RefName || f->RefLength != c->RefLength) {
- cerr << "ERROR: mismatched references found in " << reader->GetFilename()
- << " expected: " << endl;
- for (BamTools::RefVector::const_iterator a = firstRefData.begin(); a != firstRefData.end(); ++a)
- cerr << a->RefName << " " << a->RefLength << endl;
- cerr << "but found: " << endl;
- for (BamTools::RefVector::const_iterator a = currentRefData.begin(); a != currentRefData.end(); ++a)
- cerr << a->RefName << " " << a->RefLength << endl;
- exit(1);
- }
- ++f; ++c;
- }
- }
-}
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