// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 17 January 2011 (DB)
+// Last modified: 21 March 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
m_alignments = 0;
}
-// close the BAM files
+// close all BAM files
void BamMultiReaderPrivate::Close(void) {
+ CloseFiles( Filenames() );
+}
- // clear out alignment cache
- m_alignments->Clear();
-
- // iterate over readers
- vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
- vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
- for ( ; readerIter != readerEnd; ++readerIter ) {
+// close requested BAM file
+void BamMultiReaderPrivate::CloseFile(const string& filename) {
+ vector<string> filenames(1, filename);
+ CloseFiles(filenames);
+}
- // close reader
- BamReader* reader = (*readerIter).first;
- BamAlignment* alignment = (*readerIter).second;
- if ( reader ) reader->Close();
+// close requested BAM files
+void BamMultiReaderPrivate::CloseFiles(const vector<string>& filenames) {
- // delete pointers
- delete reader;
- reader = 0;
- delete alignment;
- alignment = 0;
+ // iterate over filenames
+ vector<string>::const_iterator filesIter = filenames.begin();
+ vector<string>::const_iterator filesEnd = filenames.end();
+ for ( ; filesIter != filesEnd; ++filesIter ) {
+ const string& filename = (*filesIter);
+ if ( filename.empty() ) continue;
+
+ // iterate over readers
+ vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
+ vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ BamReader* reader = (*readerIter).first;
+ if ( reader == 0 ) continue;
+
+ // if reader matches requested filename
+ if ( reader->GetFilename() == filename ) {
+
+ // remove reader/alignment from alignment cache
+ m_alignments->Remove(reader);
+
+ // close & delete reader
+ reader->Close();
+ delete reader;
+ reader = 0;
+
+ // delete reader's alignment entry
+ BamAlignment* alignment = (*readerIter).second;
+ delete alignment;
+ alignment = 0;
+
+ // remove reader from container
+ m_readers.erase(readerIter);
+
+ // on match, just go on to next filename
+ // (no need to keep looking and iterator is invalid now anyway)
+ break;
+ }
+ }
}
- // clear out readers
- m_readers.clear();
-
- // reset default flags
- m_isCoreMode = false;
- m_sortOrder = BamMultiReader::SortedByPosition;
+ // make sure alignment cache is cleared if all readers are now closed
+ if ( m_readers.empty() && m_alignments != 0 )
+ m_alignments->Clear();
}
-// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
-bool BamMultiReaderPrivate::CreateIndexes(bool useStandardIndex) {
+// creates index files for BAM files that don't have them
+bool BamMultiReaderPrivate::CreateIndexes(const BamIndex::IndexType& type) {
bool result = true;
+
+ // iterate over readers
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
- result &= reader->CreateIndex(useStandardIndex);
+ if ( reader == 0 ) continue;
+
+ // if reader doesn't have an index, create one
+ if ( !reader->HasIndex() )
+ result &= reader->CreateIndex(type);
}
+
return result;
}
case ( BamMultiReader::SortedByPosition ) : return new PositionMultiMerger;
case ( BamMultiReader::SortedByReadName ) : return new ReadNameMultiMerger;
case ( BamMultiReader::Unsorted ) : return new UnsortedMultiMerger;
- default : //print error
+ default :
+ cerr << "BamMultiReader ERROR: requested sort order is unknown" << endl;
return 0;
}
}
return readGroup;
}
+const vector<string> BamMultiReaderPrivate::Filenames(void) const {
+
+ // init filename container
+ vector<string> filenames;
+ filenames.reserve( m_readers.size() );
+
+ // iterate over readers
+ vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin();
+ vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ const BamReader* reader = (*readerIter).first;
+ if ( reader == 0 ) continue;
+
+ // store filename if not empty
+ const string filename = reader->GetFilename();
+ if ( !filename.empty() )
+ filenames.push_back( reader->GetFilename() );
+ }
+
+ // return result
+ return filenames;
+}
+
+SamHeader BamMultiReaderPrivate::GetHeader(void) const {
+ string text = GetHeaderText();
+ return SamHeader(text);
+}
+
// makes a virtual, unified header for all the bam files in the multireader
-const string BamMultiReaderPrivate::GetHeaderText(void) const {
+string BamMultiReaderPrivate::GetHeaderText(void) const {
- // just spit single header out if only have one reader open
+ // if only one reader is open
if ( m_readers.size() == 1 ) {
+ // just return reader's header text
+ const ReaderAlignment& ra = m_readers.front();
+ const BamReader* reader = ra.first;
+ if ( reader ) return reader->GetHeaderText();
- vector<ReaderAlignment>::const_iterator readerBegin = m_readers.begin();
- const ReaderAlignment& entry = (*readerBegin);
- const BamReader* reader = entry.first;
- if ( reader == 0 ) return "";
- return reader->GetHeaderText();
+ // invalid reader
+ return string();
}
- string mergedHeader = "";
+ string mergedHeader("");
map<string, bool> readGroups;
// foreach extraction entry (each BAM file)
vector<ReaderAlignment>::const_iterator readerIter = readerBegin;
vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
-
- // get header from reader
const BamReader* reader = (*readerIter).first;
if ( reader == 0 ) continue;
+
+ // get header from reader
string headerText = reader->GetHeaderText();
if ( headerText.empty() ) continue;
// get next line from header, skip if empty
const string headerLine = (*linesIter);
- if ( headerLine.empty() ) { continue; }
+ if ( headerLine.empty() ) continue;
// if first file, save HD & SQ entries
+ // TODO: what if first file has empty header, should just check for empty 'mergedHeader' instead ?
if ( readerIter == readerBegin ) {
if ( headerLine.find("@HD") == 0 || headerLine.find("@SQ") == 0) {
mergedHeader.append(headerLine.c_str());
// 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;
+ cerr << "BamMultiReader WARNING: duplicate @RG tag " << readGroup
+ << " entry in header of " << reader->GetFilename() << endl;
}
}
}
// get next alignment among all files
bool BamMultiReaderPrivate::GetNextAlignment(BamAlignment& al) {
- return LoadNextAlignment(al, false);
+ m_isCoreMode = false;
+ return LoadNextAlignment(al);
}
// get next alignment among all files without parsing character data from alignments
bool BamMultiReaderPrivate::GetNextAlignmentCore(BamAlignment& al) {
- return LoadNextAlignment(al, true);
+ m_isCoreMode = true;
+ return LoadNextAlignment(al);
}
// ---------------------------------------------------------------------------------------
//
// 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.
+// references for all BAM files. We enforce this by invoking the
+// ValidateReaders() method 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 BamMultiReaderPrivate::GetReferenceCount(void) const {
- const ReaderAlignment& firstReader = m_readers.front();
- const BamReader* reader = firstReader.first;
+int BamMultiReaderPrivate::GetReferenceCount(void) const {
+
+ // handle empty multireader
+ if ( m_readers.empty() )
+ return 0;
+
+ // return reference count from first reader
+ const ReaderAlignment& ra = m_readers.front();
+ const BamReader* reader = ra.first;
if ( reader ) return reader->GetReferenceCount();
- else return 0;
+
+ // invalid reader
+ return 0;
}
// returns vector of reference objects
const RefVector BamMultiReaderPrivate::GetReferenceData(void) const {
- const ReaderAlignment& firstReader = m_readers.front();
- const BamReader* reader = firstReader.first;
+
+ // handle empty multireader
+ if ( m_readers.empty() )
+ return RefVector();
+
+ // return reference data from first BamReader
+ const ReaderAlignment& ra = m_readers.front();
+ const BamReader* reader = ra.first;
if ( reader ) return reader->GetReferenceData();
- else return RefVector();
+
+ // invalid reader
+ return RefVector();
}
// returns refID from reference name
-const int BamMultiReaderPrivate::GetReferenceID(const string& refName) const {
- const ReaderAlignment& firstReader = m_readers.front();
- const BamReader* reader = firstReader.first;
+int BamMultiReaderPrivate::GetReferenceID(const string& refName) const {
+
+ // handle empty multireader
+ if ( m_readers.empty() )
+ return -1;
+
+ // return reference ID from first BamReader
+ const ReaderAlignment& ra = m_readers.front();
+ const BamReader* reader = ra.first;
if ( reader ) return reader->GetReferenceID(refName);
- else return -1; // ERROR case - how to report
-}
+ // invalid reader
+ return -1;
+}
// ---------------------------------------------------------------------------------------
// checks if any readers still have alignments
-bool BamMultiReaderPrivate::HasOpenReaders(void) {
- return ( m_alignments->Size() > 0 );
+bool BamMultiReaderPrivate::HasAlignmentData(void) const {
+ if ( m_alignments == 0 )
+ return false;
+ return !m_alignments->IsEmpty();
}
-// returns whether underlying BAM readers ALL have an index loaded
+// returns true if all readers have index data available
// this is useful to indicate whether Jump() or SetRegion() are possible
-bool BamMultiReaderPrivate::IsIndexLoaded(void) const {
- bool ok = true;
+bool BamMultiReaderPrivate::HasIndexes(void) const {
+
+ // handle empty multireader
+ if ( m_readers.empty() )
+ return false;
+
+ bool result = true;
+
+ // iterate over readers
+ vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin();
+ vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ const BamReader* reader = (*readerIter).first;
+ if ( reader == 0 ) continue;
+
+ // see if current reader has index data
+ result &= reader->HasIndex();
+ }
+
+ return result;
+}
+
+// returns true if multireader has open readers
+bool BamMultiReaderPrivate::HasOpenReaders(void) {
+
+ // iterate over readers
vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
const BamReader* reader = (*readerIter).first;
- if ( reader ) ok &= reader->IsIndexLoaded();
+ if ( reader == 0 ) continue;
+
+ // return true whenever an open reader is found
+ if ( reader->IsOpen() ) return true;
}
- return ok;
+
+ // no readers open
+ return false;
}
-// jumps to specified region(refID, leftBound) in BAM files, returns success/fail
+// performs random-access jump using (refID, position) as a left-bound
bool BamMultiReaderPrivate::Jump(int refID, int position) {
- bool ok = true;
+ // NB: While it may make sense to track readers in which we can
+ // successfully Jump, in practice a failure of Jump means "no
+ // alignments here." It makes sense to simply accept the failure,
+ // UpdateAlignments(), and continue.
+
+ // iterate over readers
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
if ( reader == 0 ) continue;
- ok &= reader->Jump(refID, position);
- if ( !ok ) {
- cerr << "ERROR: could not jump " << reader->GetFilename()
+ // attempt jump() on each
+ if ( !reader->Jump(refID, position) ) {
+ cerr << "BamMultiReader ERROR: could not jump " << reader->GetFilename()
<< " to " << refID << ":" << position << endl;
- exit(1);
}
}
- if (ok) UpdateAlignments();
- return ok;
+ // update alignment cache & return success
+ UpdateAlignmentCache();
+ return true;
}
-bool BamMultiReaderPrivate::LoadNextAlignment(BamAlignment& al, bool coreMode) {
+bool BamMultiReaderPrivate::LoadNextAlignment(BamAlignment& al) {
// bail out if no more data to process
- if ( !HasOpenReaders() ) return false;
+ if ( !HasAlignmentData() )
+ return false;
// "pop" next alignment and reader
ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst();
- BamReader* reader = nextReaderAlignment.first;
+ BamReader* reader = nextReaderAlignment.first;
BamAlignment* alignment = nextReaderAlignment.second;
- // save it by copy to our argument
- al = BamAlignment(*alignment);
+ // store cached alignment into destination parameter (by copy)
+ al = *alignment;
// peek to next alignment & store in cache
- m_isCoreMode = coreMode;
- SaveNextAlignment(reader,alignment);
+ SaveNextAlignment(reader, alignment);
// return success
return true;
}
-// opens BAM files
-bool BamMultiReaderPrivate::Open(const vector<string>& filenames,
- bool openIndexes,
- bool coreMode,
- bool preferStandardIndex)
-{
- // store core mode flag
- m_isCoreMode = coreMode;
-
- // first clear out any prior alignment cache prior data
- if ( m_alignments ) {
- m_alignments->Clear();
- delete m_alignments;
- m_alignments = 0;
+// locate (& load) index files for BAM readers that don't already have one loaded
+bool BamMultiReaderPrivate::LocateIndexes(const BamIndex::IndexType& preferredType) {
+
+ bool result = true;
+
+ // iterate over readers
+ vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
+ vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ BamReader* reader = (*readerIter).first;
+ if ( reader == 0 ) continue;
+
+ // if reader has no index, try to locate one
+ if ( !reader->HasIndex() )
+ result &= reader->LocateIndex(preferredType);
}
- // create alignment cache based on sorting mode
- m_alignments = CreateMergerForCurrentSortOrder();
- if ( m_alignments == 0 ) return false;
+ return result;
+}
+
+// opens BAM files
+bool BamMultiReaderPrivate::Open(const vector<string>& filenames) {
+
+ // create alignment cache if neccessary
+ if ( m_alignments == 0 ) {
+ m_alignments = CreateMergerForCurrentSortOrder();
+ if ( m_alignments == 0 ) return false;
+ }
// iterate over filenames
vector<string>::const_iterator filenameIter = filenames.begin();
vector<string>::const_iterator filenameEnd = filenames.end();
for ( ; filenameIter != filenameEnd; ++filenameIter ) {
- const string filename = (*filenameIter);
+ const string& filename = (*filenameIter);
+ if ( filename.empty() ) continue;
- bool openedOk = true;
- BamReader* reader = new BamReader;
- openedOk = reader->Open(filename, "", openIndexes, preferStandardIndex);
+ // attempt to open BamReader on filename
+ BamReader* reader = OpenReader(filename);
+ if ( reader == 0 ) continue;
- // if file opened ok
- if ( openedOk ) {
+ // store reader with new alignment
+ m_readers.push_back( make_pair(reader, new BamAlignment) );
+ }
- // try to read first alignment
- bool fileOk = true;
- BamAlignment* alignment = new BamAlignment;
- fileOk &= ( coreMode ? reader->GetNextAlignmentCore(*alignment)
- : reader->GetNextAlignment(*alignment) );
+ // validate & rewind any opened readers, also refreshes alignment cache
+ if ( !m_readers.empty() ) {
+ ValidateReaders();
+ Rewind();
+ }
- if ( fileOk ) {
+ // return success
+ return true;
+}
- m_readers.push_back( make_pair(reader, alignment) );
- m_alignments->Add( make_pair(reader, alignment) );
+bool BamMultiReaderPrivate::OpenFile(const std::string& filename) {
+ vector<string> filenames(1, filename);
+ return Open(filenames);
+}
- } else {
- cerr << "WARNING: could not read first alignment in "
- << filename << ", ignoring file" << endl;
+bool BamMultiReaderPrivate::OpenIndexes(const vector<string>& indexFilenames) {
- // if only file available & could not be read, return failure
- if ( filenames.size() == 1 )
- return false;
- }
+ // TODO: This needs to be cleaner - should not assume same order.
+ // And either way, shouldn't start at first reader. Should start at
+ // first reader without an index?
+
+ // make sure same number of index filenames as readers
+ if ( m_readers.size() != indexFilenames.size() || !indexFilenames.empty() )
+ return false;
+
+ // init result flag
+ bool result = true;
+
+ // iterate over BamReaders
+ vector<string>::const_iterator indexFilenameIter = indexFilenames.begin();
+ vector<string>::const_iterator indexFilenameEnd = indexFilenames.end();
+ vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
+ vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ BamReader* reader = (*readerIter).first;
+
+ // open index filename on reader
+ if ( reader ) {
+ const string& indexFilename = (*indexFilenameIter);
+ result &= reader->OpenIndex(indexFilename);
+ }
+
+ // increment filename iterator, skip if no more index files to open
+ if ( ++indexFilenameIter == indexFilenameEnd )
+ break;
+ }
+
+ // TODO: validation ??
+
+ // return success/fail
+ return result;
+}
+
+BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) {
+
+ // create new BamReader
+ BamReader* reader = new BamReader;
+
+ // if reader opens OK
+ if ( reader->Open(filename) ) {
+
+ // attempt to read first alignment (sanity check)
+ // if ok, then return BamReader pointer
+ BamAlignment al;
+ if ( reader->GetNextAlignmentCore(al) )
+ return reader;
+
+ // could not read alignment
+ else {
+ cerr << "BamMultiReader WARNING: Could not read first alignment from "
+ << filename << ", ignoring file" << endl;
}
+ }
- // TODO; any further error handling when openedOK is false ??
- else return false;
+ // reader could not open
+ else {
+ cerr << "BamMultiReader WARNING: Could not open: "
+ << filename << ", ignoring file" << endl;
}
- // files opened ok, at least one alignment could be read,
- // now need to check that all files use same reference data
- ValidateReaders();
- return true;
+ // if we get here, there was a problem with this BAM file (opening or reading)
+ // clean up memory allocation & return null pointer
+ delete reader;
+ return 0;
}
// print associated filenames to stdout
void BamMultiReaderPrivate::PrintFilenames(void) const {
+ const vector<string>& filenames = Filenames();
+ vector<string>::const_iterator filenameIter = filenames.begin();
+ vector<string>::const_iterator filenameEnd = filenames.end();
+ for ( ; filenameIter != filenameEnd; ++filenameIter )
+ cout << (*filenameIter) << endl;
+}
- vector<ReaderAlignment>::const_iterator readerIter = m_readers.begin();
- vector<ReaderAlignment>::const_iterator readerEnd = m_readers.end();
- for ( ; readerIter != readerEnd; ++readerIter ) {
- const BamReader* reader = (*readerIter).first;
- if ( reader == 0 ) continue;
- cout << reader->GetFilename() << endl;
+// returns BAM file pointers to beginning of alignment data & resets alignment cache
+bool BamMultiReaderPrivate::Rewind(void) {
+
+ // clear out alignment cache
+ m_alignments->Clear();
+
+ // attempt to rewind files
+ if ( !RewindReaders() ) {
+ cerr << "BamMultiReader ERROR: could not rewind file(s) successfully";
+ return false;
}
+
+ // reset cache & return success
+ UpdateAlignmentCache();
+ return true;
}
// returns BAM file pointers to beginning of alignment data
-bool BamMultiReaderPrivate::Rewind(void) {
+bool BamMultiReaderPrivate::RewindReaders(void) {
bool result = true;
+
+ // iterate over readers
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
if ( reader == 0 ) continue;
+
+ // attempt rewind on BamReader
result &= reader->Rewind();
}
+
return result;
}
}
// sets the index caching mode on the readers
-void BamMultiReaderPrivate::SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode) {
+void BamMultiReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode mode) {
+ // iterate over readers
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
if ( reader == 0 ) continue;
+
+ // set reader's index cache mode
reader->SetIndexCacheMode(mode);
}
}
// alignments here." It makes sense to simply accept the failure,
// UpdateAlignments(), and continue.
+ // iterate over alignments
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
if ( reader == 0 ) continue;
+
+ // attempt to set BamReader's region of interest
if ( !reader->SetRegion(region) ) {
- cerr << "ERROR: could not jump " << reader->GetFilename() << " to "
+ cerr << "BamMultiReader ERROR: could not jump " << reader->GetFilename() << " to "
<< region.LeftRefID << ":" << region.LeftPosition << ".."
<< region.RightRefID << ":" << region.RightPosition << endl;
}
}
- UpdateAlignments();
+ // update alignment cache & return success
+ UpdateAlignmentCache();
return true;
}
// copy old cache contents to new cache
while ( m_alignments->Size() > 0 ) {
- ReaderAlignment value = m_alignments->TakeFirst();
+ ReaderAlignment value = m_alignments->TakeFirst(); // retrieves & 'pops'
newAlignmentCache->Add(value);
}
m_alignments = newAlignmentCache;
}
+// splits the entire header into a list of strings
+const vector<string> BamMultiReaderPrivate::SplitHeaderText(const string& headerText) const {
+
+ stringstream header(headerText);
+ string item;
+
+ vector<string> lines;
+ while ( getline(header, item) )
+ lines.push_back(item);
+ return lines;
+}
+
// updates our alignment cache
-void BamMultiReaderPrivate::UpdateAlignments(void) {
+void BamMultiReaderPrivate::UpdateAlignmentCache(void) {
+
+ // skip if invalid alignment cache
+ if ( m_alignments == 0 ) return;
// clear the cache
m_alignments->Clear();
+ // seed cache with fully-populated alignments
+ // further updates will fill with full/core-only as requested
+ m_isCoreMode = false;
+
// iterate over readers
vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
vector<ReaderAlignment>::iterator readerEnd = m_readers.end();
for ( ; readerIter != readerEnd; ++readerIter ) {
BamReader* reader = (*readerIter).first;
BamAlignment* alignment = (*readerIter).second;
- if ( reader == 0 ) continue;
+ if ( reader == 0 || alignment == 0 ) continue;
+
+ // save next alignment from each reader in cache
SaveNextAlignment(reader, alignment);
}
}
-// splits the entire header into a list of strings
-const vector<string> BamMultiReaderPrivate::SplitHeaderText(const string& headerText) const {
- stringstream header(headerText);
- vector<string> lines;
- string item;
- while ( getline(header, item) )
- lines.push_back(item);
- return lines;
-}
-
// 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
// retrieve first reader data
const BamReader* firstReader = m_readers.front().first;
- if ( firstReader == 0 ) return; // signal error?
+ if ( firstReader == 0 ) return;
const RefVector firstReaderRefData = firstReader->GetReferenceData();
const int firstReaderRefCount = firstReader->GetReferenceCount();
const int firstReaderRefSize = firstReaderRefData.size();
// get current reader data
BamReader* reader = (*readerIter).first;
- if ( reader == 0 ) continue; // error?
+ if ( reader == 0 ) continue;
const RefVector currentReaderRefData = reader->GetReferenceData();
const int currentReaderRefCount = reader->GetReferenceCount();
const int currentReaderRefSize = currentReaderRefData.size();
if ( (currentReaderRefCount != firstReaderRefCount) ||
(firstReaderRefSize != currentReaderRefSize) )
{
- cerr << "ERROR: mismatched number of references in " << reader->GetFilename()
+ cerr << "BamMultiReader ERROR: mismatched number of references in " << reader->GetFilename()
<< " expected " << firstReaderRefCount
<< " reference sequences but only found " << currentReaderRefCount << 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 ( firstRefIter != firstRefEnd ) {
-
const RefData& firstRef = (*firstRefIter);
const RefData& currentRef = (*currentRefIter);
if ( (firstRef.RefName != currentRef.RefName) ||
(firstRef.RefLength != currentRef.RefLength) )
{
- cerr << "ERROR: mismatched references found in " << reader->GetFilename()
+ cerr << "BamMultiReader ERROR: mismatched references found in " << reader->GetFilename()
<< " expected: " << endl;
+
+ // print first reader's reference data
RefVector::const_iterator refIter = firstReaderRefData.begin();
RefVector::const_iterator refEnd = firstReaderRefData.end();
for ( ; refIter != refEnd; ++refIter ) {
}
cerr << "but found: " << endl;
+
+ // print current reader's reference data
refIter = currentReaderRefData.begin();
refEnd = currentReaderRefData.end();
for ( ; refIter != refEnd; ++refIter ) {
projects / bamtools.git / blobdiff