From: Derek Date: Sun, 19 Sep 2010 21:06:02 +0000 (-0400) Subject: Removed a backup text file that snuck into an earlier commit X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c98f4ce3c7c19af972f58eaf0053b94ba9413c81;p=bamtools.git Removed a backup text file that snuck into an earlier commit --- diff --git a/src/api/BamMultiReader.cpp~ b/src/api/BamMultiReader.cpp~ deleted file mode 100644 index b5c4002..0000000 --- a/src/api/BamMultiReader.cpp~ +++ /dev/null @@ -1,450 +0,0 @@ -// *************************************************************************** -// 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 -#include -#include -#include -#include -#include -#include -#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 >::iterator readerIter = readers.begin(); - vector >::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 >::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 readGroups; - - // foreach extraction entry (each BAM file) - for (vector >::const_iterator rs = readers.begin(); rs != readers.end(); ++rs) { - - BamReader* reader = rs->first; - const string headerText = reader->GetHeaderText(); - if ( headerText.empty() ) continue; - - map currentFileReadGroups; - stringstream header(headerText); - vector lines; - string item; - while (getline(header, item)) - lines.push_back(item); - - for (vector::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 >::const_iterator readerIter = readers.begin(); - vector >::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 >::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& filenames, bool openIndexes, bool coreMode, bool useDefaultIndex) { - - // for filename in filenames - fileNames = filenames; // save filenames in our multireader - for (vector::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 >::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 >::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 >::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 >::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 >::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; - } - } -}