// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 19 September 2010 (DB)
+// Last modified: 20 September 2010 (DB)
// ---------------------------------------------------------------------------
//
// ***************************************************************************
// internal methods
private:
+ // close & delete BamWriters in map
+ template<typename T>
+ void CloseWriters(map<T, BamWriter*>& writers);
+ // calculate output stub based on IO args given
void DetermineOutputFilenameStub(void);
+ // open our BamReader
bool OpenReader(void);
+ // split alignments in BAM file based on isMapped property
bool SplitMapped(void);
+ // split alignments in BAM file based on isPaired property
bool SplitPaired(void);
+ // split alignments in BAM file based on refID property
bool SplitReference(void);
+ // finds first alignment and calls corresponding SplitTagImpl<>
+ // depending on tag type
bool SplitTag(void);
- bool SplitTag_Int(BamAlignment& al);
- bool SplitTag_UInt(BamAlignment& al);
- bool SplitTag_Real(BamAlignment& al);
- bool SplitTag_String(BamAlignment& al);
+ // templated split tag implementation
+ // handle the various types that are possible for tags
+ template<typename T>
+ bool SplitTagImpl(BamAlignment& al);
// data members
private:
}
// clean up BamWriters
- map<bool, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin() ; writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if ( writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
+ CloseWriters(outputFiles);
// return success
return true;
}
// clean up BamWriters
- map<bool, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin() ; writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if (writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
+ CloseWriters(outputFiles);
// return success
return true;
}
// clean up BamWriters
- map<int32_t, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin(); writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if (writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
+ CloseWriters(outputFiles);
// return success
return true;
}
+// finds first alignment and calls corresponding SplitTagImpl<>() depending on tag type
bool SplitTool::SplitToolPrivate::SplitTag(void) {
// iterate through alignments, until we hit TAG
case 'c' :
case 's' :
case 'i' :
- return SplitTag_Int(al);
+ return SplitTagImpl<int32_t>(al);
case 'C' :
case 'S' :
case 'I' :
- return SplitTag_UInt(al);
+ return SplitTagImpl<uint32_t>(al);
case 'f' :
- return SplitTag_Real(al);
+ return SplitTagImpl<float>(al);
case 'A':
case 'Z':
case 'H':
- return SplitTag_String(al);
+ return SplitTagImpl<string>(al);
default:
fprintf(stderr, "ERROR: Unknown tag storage class encountered: [%c]\n", tagType);
return true;
}
-bool SplitTool::SplitToolPrivate::SplitTag_Int(BamAlignment& al) {
-
- // set up splitting data structure
- map<int32_t, BamWriter*> outputFiles;
- map<int32_t, BamWriter*>::iterator writerIter;
-
- // local variables
- const string tag = m_settings->TagToSplit;
- BamWriter* writer;
- stringstream outputFilenameStream("");
- int32_t currentValue;
-
- // retrieve first alignment tag value
- if ( al.GetTag(tag, currentValue) ) {
-
- // open new BamWriter, save first alignment
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
- writer->SaveAlignment(al);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- }
-
- // iterate through remaining alignments
- while ( m_reader.GetNextAlignment(al) ) {
-
- // skip if this alignment doesn't have TAG
- if ( !al.GetTag(tag, currentValue) ) continue;
-
- // look up tag value in map
- writerIter = outputFiles.find(currentValue);
-
- // if no writer associated with this value
- if ( writerIter == outputFiles.end() ) {
-
- // open new BamWriter
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- }
-
- // else grab corresponding writer
- else writer = (*writerIter).second;
-
- // store alignment in proper BAM output file
- if ( writer )
- writer->SaveAlignment(al);
- }
-
- // clean up BamWriters
- map<int32_t, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin(); writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if (writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
-
- // return success
- return true;
-}
+// --------------------------------------------------------------------------------
+// template method implementation
+// N.B. - *technical note* - use of template methods defined in ".cpp" goes against normal practices
+// but works here because these are purely internal (no one can call from outside this file)
-bool SplitTool::SplitToolPrivate::SplitTag_UInt(BamAlignment& al) {
+// close BamWriters & delete pointers
+template<typename T>
+void SplitTool::SplitToolPrivate::CloseWriters(map<T, BamWriter*>& writers) {
- // set up splitting data structure
- map<uint32_t, BamWriter*> outputFiles;
- map<uint32_t, BamWriter*>::iterator writerIter;
-
- // local variables
- const string tag = m_settings->TagToSplit;
- BamWriter* writer;
- stringstream outputFilenameStream("");
- uint32_t currentValue;
-
- int alignmentsIgnored = 0;
-
- // retrieve first alignment tag value
- if ( al.GetTag(tag, currentValue) ) {
-
- // open new BamWriter, save first alignment
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
- writer->SaveAlignment(al);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- } else ++alignmentsIgnored;
-
- // iterate through remaining alignments
- while ( m_reader.GetNextAlignment(al) ) {
-
- // skip if this alignment doesn't have TAG
- if ( !al.GetTag(tag, currentValue) ) { ++alignmentsIgnored; continue; }
-
- // look up tag value in map
- writerIter = outputFiles.find(currentValue);
-
- // if no writer associated with this value
- if ( writerIter == outputFiles.end() ) {
-
- // open new BamWriter
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- }
-
- // else grab corresponding writer
- else writer = (*writerIter).second;
-
- // store alignment in proper BAM output file
- if ( writer )
- writer->SaveAlignment(al);
- }
-
- // clean up BamWriters
- map<uint32_t, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin(); writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if (writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
-
- // return success
- return true;
-}
-
-bool SplitTool::SplitToolPrivate::SplitTag_Real(BamAlignment& al) {
-
- // set up splitting data structure
- map<float, BamWriter*> outputFiles;
- map<float, BamWriter*>::iterator writerIter;
-
- // local variables
- const string tag = m_settings->TagToSplit;
- BamWriter* writer;
- stringstream outputFilenameStream("");
- float currentValue;
-
- // retrieve first alignment tag value
- if ( al.GetTag(tag, currentValue) ) {
-
- // open new BamWriter, save first alignment
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
- writer->SaveAlignment(al);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- }
-
- // iterate through remaining alignments
- while ( m_reader.GetNextAlignment(al) ) {
-
- // skip if this alignment doesn't have TAG
- if ( !al.GetTag(tag, currentValue) ) continue;
-
- // look up tag value in map
- writerIter = outputFiles.find(currentValue);
-
- // if no writer associated with this value
- if ( writerIter == outputFiles.end() ) {
-
- // open new BamWriter
- writer = new BamWriter;
- outputFilenameStream << m_outputFilenameStub << ".TAG_" << tag << "_" << currentValue << ".bam";
- writer->Open(outputFilenameStream.str(), m_header, m_references);
-
- // store in map
- outputFiles.insert( make_pair(currentValue, writer) );
-
- // reset stream
- outputFilenameStream.str("");
- }
-
- // else grab corresponding writer
- else writer = (*writerIter).second;
-
- // store alignment in proper BAM output file
- if ( writer )
- writer->SaveAlignment(al);
- }
-
- // clean up BamWriters
- map<float, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin(); writerIter != writerEnd; ++writerIter ) {
+ typedef map<T, BamWriter*> WriterMap;
+ typedef typename WriterMap::iterator WriterMapIterator;
+
+ WriterMapIterator writerIter = writers.begin();
+ WriterMapIterator writerEnd = writers.end();
+ for ( ; writerIter != writerEnd; ++writerIter ) {
BamWriter* writer = (*writerIter).second;
if (writer == 0 ) continue;
writer->Close();
delete writer;
writer = 0;
}
-
- // return success
- return true;
+ writers.clear();
}
-bool SplitTool::SplitToolPrivate::SplitTag_String(BamAlignment& al) {
+// handle the various types that are possible for tags
+template<typename T>
+bool SplitTool::SplitToolPrivate::SplitTagImpl(BamAlignment& al) {
- // set up splitting data structure
- map<string, BamWriter*> outputFiles;
- map<string, BamWriter*>::iterator writerIter;
+ typedef T TagValueType;
+ typedef map<TagValueType, BamWriter*> WriterMap;
+ typedef typename WriterMap::iterator WriterMapIterator;
+
+ // set up splitting data structure
+ WriterMap outputFiles;
+ WriterMapIterator writerIter;
// local variables
const string tag = m_settings->TagToSplit;
BamWriter* writer;
stringstream outputFilenameStream("");
- string currentValue;
+ TagValueType currentValue;
// retrieve first alignment tag value
if ( al.GetTag(tag, currentValue) ) {
writer->SaveAlignment(al);
}
- // clean up BamWriters
- map<string, BamWriter*>::iterator writerEnd = outputFiles.end();
- for ( writerIter = outputFiles.begin(); writerIter != writerEnd; ++writerIter ) {
- BamWriter* writer = (*writerIter).second;
- if (writer == 0 ) continue;
- writer->Close();
- delete writer;
- writer = 0;
- }
+ // clean up BamWriters
+ CloseWriters(outputFiles);
// return success
- return true;
+ return true;
}
// ---------------------------------------------
projects / bamtools.git / commitdiff