From: derek Date: Sat, 10 Sep 2011 02:05:02 +0000 (-0400) Subject: Merge branches 'master' and 'iodevice' into iodevice X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c1fc1c5423ca73a1b5bcbe790650821d73e5959c;hp=57ff487e7acaf7f55a45c0a80cb9647bb1d83801;p=bamtools.git Merge branches 'master' and 'iodevice' into iodevice --- diff --git a/README b/README index 1780ede..498f4be 100644 --- a/README +++ b/README @@ -56,6 +56,5 @@ Derek Barnett Marth Lab Biology Dept., Boston College -Email: barnetde@bc.edu -Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT) - http://sourceforge.net/projects/bamtools (major updates only) +Email: derekwbarnett@gmail.com +Project Website: http://github.com/pezmaster31/bamtools diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp index 0077f64..91ca8ad 100644 --- a/src/api/BamAlignment.cpp +++ b/src/api/BamAlignment.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamAlignment.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 22 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h index 7535d93..aa1d940 100644 --- a/src/api/BamAlignment.h +++ b/src/api/BamAlignment.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamAlignment.h (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 22 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamAux.h b/src/api/BamAux.h index d171e70..4c5a99a 100644 --- a/src/api/BamAux.h +++ b/src/api/BamAux.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 4 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h index 00a8f01..a52922e 100644 --- a/src/api/BamIndex.h +++ b/src/api/BamIndex.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamIndex.h (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp index 06055df..8543451 100644 --- a/src/api/BamMultiReader.cpp +++ b/src/api/BamMultiReader.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 15 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index cc49ec8..561ce7a 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 15 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp index eaa6882..4b25b15 100644 --- a/src/api/BamReader.cpp +++ b/src/api/BamReader.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 4 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamReader.h b/src/api/BamReader.h index 85b0c0d..836fbf5 100644 --- a/src/api/BamReader.h +++ b/src/api/BamReader.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 4 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp index 8582f34..8bf6f18 100644 --- a/src/api/BamWriter.cpp +++ b/src/api/BamWriter.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 4 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h index 476dbec..56ac301 100644 --- a/src/api/BamWriter.h +++ b/src/api/BamWriter.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 4 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h index d345920..913c213 100644 --- a/src/api/SamConstants.h +++ b/src/api/SamConstants.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamConstants.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp index 9104978..77e1c6d 100644 --- a/src/api/SamHeader.cpp +++ b/src/api/SamHeader.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamHeader.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h index 5c7a101..3b67621 100644 --- a/src/api/SamHeader.h +++ b/src/api/SamHeader.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamHeader.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp index b89a10b..fed9b8b 100644 --- a/src/api/SamProgram.cpp +++ b/src/api/SamProgram.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamProgram.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamProgram.h b/src/api/SamProgram.h index 3c89059..97a9ae5 100644 --- a/src/api/SamProgram.h +++ b/src/api/SamProgram.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamProgram.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamProgramChain.cpp b/src/api/SamProgramChain.cpp index 66b7f07..287dcdf 100644 --- a/src/api/SamProgramChain.cpp +++ b/src/api/SamProgramChain.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamProgramChain.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamProgramChain.h b/src/api/SamProgramChain.h index 4cb16fc..02f0237 100644 --- a/src/api/SamProgramChain.h +++ b/src/api/SamProgramChain.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamProgramChain.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp index 2ba75f1..a9170d7 100644 --- a/src/api/SamReadGroup.cpp +++ b/src/api/SamReadGroup.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamReadGroup.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamReadGroup.h b/src/api/SamReadGroup.h index b203d3c..b1fbfb8 100644 --- a/src/api/SamReadGroup.h +++ b/src/api/SamReadGroup.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamReadGroup.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp index 69903ff..f243f92 100644 --- a/src/api/SamReadGroupDictionary.cpp +++ b/src/api/SamReadGroupDictionary.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamReadGroupDictionary.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamReadGroupDictionary.h b/src/api/SamReadGroupDictionary.h index 8ec40e2..328763a 100644 --- a/src/api/SamReadGroupDictionary.h +++ b/src/api/SamReadGroupDictionary.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamReadGroupDictionary.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp index 0231988..c8e375f 100644 --- a/src/api/SamSequence.cpp +++ b/src/api/SamSequence.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamSequence.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h index 054e58f..6f1a2ab 100644 --- a/src/api/SamSequence.h +++ b/src/api/SamSequence.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamSequence.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamSequenceDictionary.cpp b/src/api/SamSequenceDictionary.cpp index 3e5240d..10d0437 100644 --- a/src/api/SamSequenceDictionary.cpp +++ b/src/api/SamSequenceDictionary.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamSequenceDictionary.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/SamSequenceDictionary.h b/src/api/SamSequenceDictionary.h index 1ac7326..76bd45a 100644 --- a/src/api/SamSequenceDictionary.h +++ b/src/api/SamSequenceDictionary.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamSequenceDictionary.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 // --------------------------------------------------------------------------- diff --git a/src/api/api_global.h b/src/api/api_global.h index 84fcad2..f1c2353 100644 --- a/src/api/api_global.h +++ b/src/api/api_global.h @@ -1,7 +1,6 @@ // *************************************************************************** // api_global.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/BamHeader_p.cpp index 2f4ef34..45dc379 100644 --- a/src/api/internal/BamHeader_p.cpp +++ b/src/api/internal/BamHeader_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamHeader_p.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 21 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamHeader_p.h b/src/api/internal/BamHeader_p.h index 1f1a31c..3738c60 100644 --- a/src/api/internal/BamHeader_p.h +++ b/src/api/internal/BamHeader_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamHeader_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 26 January 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp index 69b372b..c91f433 100644 --- a/src/api/internal/BamIndexFactory_p.cpp +++ b/src/api/internal/BamIndexFactory_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamIndexFactory_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamIndexFactory_p.h b/src/api/internal/BamIndexFactory_p.h index f060d2c..7b1ff96 100644 --- a/src/api/internal/BamIndexFactory_p.h +++ b/src/api/internal/BamIndexFactory_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamIndexFactory_p.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h index ae67eea..15ae437 100644 --- a/src/api/internal/BamMultiMerger_p.h +++ b/src/api/internal/BamMultiMerger_p.h @@ -1,9 +1,8 @@ // *************************************************************************** // BamMultiMerger_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 18 March 2011 (DB) +// Last modified: 9 September 2011 (DB) // --------------------------------------------------------------------------- // Provides merging functionality for BamMultiReader. At this point, supports // sorting results by (refId, position) or by read name. @@ -42,7 +41,7 @@ class IBamMultiMerger { virtual ~IBamMultiMerger(void) { } public: - virtual void Add(const ReaderAlignment& value) =0; + virtual void Add(ReaderAlignment value) =0; virtual void Clear(void) =0; virtual const ReaderAlignment& First(void) const =0; virtual bool IsEmpty(void) const =0; @@ -59,7 +58,7 @@ class PositionMultiMerger : public IBamMultiMerger { ~PositionMultiMerger(void) { } public: - void Add(const ReaderAlignment& value); + void Add(ReaderAlignment value); void Clear(void); const ReaderAlignment& First(void) const; bool IsEmpty(void) const; @@ -87,7 +86,7 @@ class ReadNameMultiMerger : public IBamMultiMerger { ~ReadNameMultiMerger(void) { } public: - void Add(const ReaderAlignment& value); + void Add(ReaderAlignment value); void Clear(void); const ReaderAlignment& First(void) const; bool IsEmpty(void) const; @@ -115,7 +114,7 @@ class UnsortedMultiMerger : public IBamMultiMerger { ~UnsortedMultiMerger(void) { } public: - void Add(const ReaderAlignment& value); + void Add(ReaderAlignment value); void Clear(void); const ReaderAlignment& First(void) const; bool IsEmpty(void) const; @@ -135,7 +134,7 @@ class UnsortedMultiMerger : public IBamMultiMerger { // ------------------------------------------ // PositionMultiMerger implementation -inline void PositionMultiMerger::Add(const ReaderAlignment& value) { +inline void PositionMultiMerger::Add(ReaderAlignment value) { const KeyType key( value.second->RefID, value.second->Position ); m_data.insert( ElementType(key, value) ); } @@ -188,9 +187,12 @@ inline ReaderAlignment PositionMultiMerger::TakeFirst(void) { // ------------------------------------------ // ReadNameMultiMerger implementation -inline void ReadNameMultiMerger::Add(const ReaderAlignment& value) { - const KeyType key(value.second->Name); - m_data.insert( ElementType(key, value) ); +inline void ReadNameMultiMerger::Add(ReaderAlignment value) { + BamAlignment* al = value.second; + if ( al->BuildCharData() ) { + const KeyType key(al->Name); + m_data.insert( ElementType(key, value) ); + } } inline void ReadNameMultiMerger::Clear(void) { @@ -242,7 +244,7 @@ inline ReaderAlignment ReadNameMultiMerger::TakeFirst(void) { // ------------------------------------------ // UnsortedMultiMerger implementation -inline void UnsortedMultiMerger::Add(const ReaderAlignment& value) { +inline void UnsortedMultiMerger::Add(ReaderAlignment value) { m_data.push_back(value); } diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp index e789d06..189f0ec 100644 --- a/src/api/internal/BamMultiReader_p.cpp +++ b/src/api/internal/BamMultiReader_p.cpp @@ -1,9 +1,8 @@ // *************************************************************************** // BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 5 April 2011 (DB) +// Last modified: 9 September 2011 (DB) // --------------------------------------------------------------------------- // Functionality for simultaneously reading multiple BAM files // ************************************************************************* @@ -25,7 +24,6 @@ using namespace std; // ctor BamMultiReaderPrivate::BamMultiReaderPrivate(void) : m_alignments(0) - , m_isCoreMode(false) , m_sortOrder(BamMultiReader::SortedByPosition) { } @@ -261,14 +259,12 @@ string BamMultiReaderPrivate::GetHeaderText(void) const { // get next alignment among all files bool BamMultiReaderPrivate::GetNextAlignment(BamAlignment& al) { - m_isCoreMode = false; - return LoadNextAlignment(al); + return PopNextCachedAlignment(al, true); } // get next alignment among all files without parsing character data from alignments bool BamMultiReaderPrivate::GetNextAlignmentCore(BamAlignment& al) { - m_isCoreMode = true; - return LoadNextAlignment(al); + return PopNextCachedAlignment(al, false); } // --------------------------------------------------------------------------------------- @@ -406,25 +402,10 @@ bool BamMultiReaderPrivate::Jump(int refID, int position) { return true; } -bool BamMultiReaderPrivate::LoadNextAlignment(BamAlignment& al) { - - // bail out if no more data to process - if ( !HasAlignmentData() ) - return false; - - // "pop" next alignment and reader - ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst(); - BamReader* reader = nextReaderAlignment.first; - BamAlignment* alignment = nextReaderAlignment.second; - - // store cached alignment into destination parameter (by copy) - al = *alignment; - - // peek to next alignment & store in cache - SaveNextAlignment(reader, alignment); - - // return success - return true; +bool BamMultiReaderPrivate::LoadNextAlignment(BamReader* reader, BamAlignment* alignment) { + // lazy building of alignment's char data, + // only populated on demand by sorting merger or client call to GetNextAlignment() + return reader->GetNextAlignmentCore(*alignment); } // locate (& load) index files for BAM readers that don't already have one loaded @@ -456,6 +437,9 @@ bool BamMultiReaderPrivate::Open(const vector& filenames) { if ( m_alignments == 0 ) return false; } + // put all current readers back at beginning (refreshes alignment cache) + Rewind(); + // iterate over filenames vector::const_iterator filenameIter = filenames.begin(); vector::const_iterator filenameEnd = filenames.end(); @@ -464,18 +448,17 @@ bool BamMultiReaderPrivate::Open(const vector& filenames) { if ( filename.empty() ) continue; // attempt to open BamReader on filename - BamReader* reader = OpenReader(filename); - if ( reader == 0 ) continue; - - // store reader with new alignment - m_readers.push_back( make_pair(reader, new BamAlignment) ); + bool openedOk = false; + ReaderAlignment ra = OpenReader(filename, &openedOk); + if ( openedOk ) { + m_readers.push_back(ra); // store reader/alignment in local list + m_alignments->Add(ra); // add reader/alignment to sorting cache + } } - // validate & rewind any opened readers, also refreshes alignment cache - if ( !m_readers.empty() ) { + // if more than one reader open, check for reference consistency + if ( m_readers.size() > 1 ) ValidateReaders(); - Rewind(); - } // return success return true; @@ -524,19 +507,23 @@ bool BamMultiReaderPrivate::OpenIndexes(const vector& indexFilenames) { return result; } -BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) { +ReaderAlignment BamMultiReaderPrivate::OpenReader(const string& filename, bool* ok) { + + // clear status flag + *ok = false; - // create new BamReader + // create new BamReader & BamAlignment BamReader* reader = new BamReader; + BamAlignment* alignment = new BamAlignment; // 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; + // if first alignment reads OK + if ( LoadNextAlignment(reader, alignment) ) { + *ok = true; + return make_pair(reader, alignment); + } // could not read alignment else { @@ -554,7 +541,8 @@ BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) { // 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; + delete alignment; + return ReaderAlignment(); } // print associated filenames to stdout @@ -566,6 +554,33 @@ void BamMultiReaderPrivate::PrintFilenames(void) const { cout << (*filenameIter) << endl; } +bool BamMultiReaderPrivate::PopNextCachedAlignment(BamAlignment& al, const bool needCharData) { + + // bail out if no more data to process + if ( !HasAlignmentData() ) + return false; + + // pop next reader/alignment pair + ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst(); + BamReader* reader = nextReaderAlignment.first; + BamAlignment* alignment = nextReaderAlignment.second; + + // store cached alignment into destination parameter (by copy) + al = *alignment; + + // set char data if requested + if ( needCharData ) { + al.BuildCharData(); + al.Filename = reader->GetFilename(); + } + + // load next alignment from reader & store in cache + SaveNextAlignment(reader, alignment); + + // return success + return true; +} + // returns BAM file pointers to beginning of alignment data & resets alignment cache bool BamMultiReaderPrivate::Rewind(void) { @@ -604,17 +619,9 @@ bool BamMultiReaderPrivate::RewindReaders(void) { void BamMultiReaderPrivate::SaveNextAlignment(BamReader* reader, BamAlignment* alignment) { - // must be in core mode && NOT sorting by read name to call GNACore() - if ( m_isCoreMode && m_sortOrder != BamMultiReader::SortedByReadName ) { - if ( reader->GetNextAlignmentCore(*alignment) ) - m_alignments->Add( make_pair(reader, alignment) ); - } - - // not in core mode and/or sorting by readname, must call GNA() - else { - if ( reader->GetNextAlignment(*alignment) ) - m_alignments->Add( make_pair(reader, alignment) ); - } + // if can read alignment from reader, store in cache + if ( LoadNextAlignment(reader, alignment) ) + m_alignments->Add( make_pair(reader, alignment) ); } // sets the index caching mode on the readers @@ -703,10 +710,6 @@ void BamMultiReaderPrivate::UpdateAlignmentCache(void) { // 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::iterator readerIter = m_readers.begin(); vector::iterator readerEnd = m_readers.end(); diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h index b34fb0c..33048eb 100644 --- a/src/api/internal/BamMultiReader_p.h +++ b/src/api/internal/BamMultiReader_p.h @@ -1,9 +1,8 @@ // *************************************************************************** // BamMultiReader_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 13 March 2011 (DB) +// Last modified: 9 September 2011 (DB) // --------------------------------------------------------------------------- // Functionality for simultaneously reading multiple BAM files // ************************************************************************* @@ -33,6 +32,10 @@ class IBamMultiMerger; class BamMultiReaderPrivate { + // typedefs + public: + typedef std::pair ReaderAlignment; + // constructor / destructor public: BamMultiReaderPrivate(void); @@ -78,21 +81,19 @@ class BamMultiReaderPrivate { IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const; const std::string ExtractReadGroup(const std::string& headerLine) const; bool HasAlignmentData(void) const; - bool LoadNextAlignment(BamAlignment& al); - BamTools::BamReader* OpenReader(const std::string& filename); + bool LoadNextAlignment(BamReader* reader, BamAlignment* alignment); + ReaderAlignment OpenReader(const std::string& filename, bool* ok); + bool PopNextCachedAlignment(BamAlignment& al, const bool needCharData); bool RewindReaders(void); - void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment); + void SaveNextAlignment(BamReader* reader, BamAlignment* alignment); const std::vector SplitHeaderText(const std::string& headerText) const; void UpdateAlignmentCache(void); void ValidateReaders(void) const; // data members - public: - typedef std::pair ReaderAlignment; + public: std::vector m_readers; - IBamMultiMerger* m_alignments; - bool m_isCoreMode; BamMultiReader::SortOrder m_sortOrder; }; diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp index 9187b3a..a44563f 100644 --- a/src/api/internal/BamRandomAccessController_p.cpp +++ b/src/api/internal/BamRandomAccessController_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamRandomAccessController_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011(DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h index 372ea4a..86af28c 100644 --- a/src/api/internal/BamRandomAccessController_p.h +++ b/src/api/internal/BamRandomAccessController_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamRandomAccessController_p.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 24 February 2011(DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp index e4e2310..384e2fe 100644 --- a/src/api/internal/BamReader_p.cpp +++ b/src/api/internal/BamReader_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamReader_p.cpp (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 10 May 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h index c0d07d8..2901e54 100644 --- a/src/api/internal/BamReader_p.h +++ b/src/api/internal/BamReader_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamReader_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp index 6d8273e..b92c47b 100644 --- a/src/api/internal/BamStandardIndex_p.cpp +++ b/src/api/internal/BamStandardIndex_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamStandardIndex.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 24 June 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/BamStandardIndex_p.h index 7123ae7..3fbc777 100644 --- a/src/api/internal/BamStandardIndex_p.h +++ b/src/api/internal/BamStandardIndex_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamStandardIndex.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 24 June 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/BamToolsIndex_p.cpp index 05d4327..f6e05ce 100644 --- a/src/api/internal/BamToolsIndex_p.cpp +++ b/src/api/internal/BamToolsIndex_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamToolsIndex.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 27 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h index 16aef8c..269792e 100644 --- a/src/api/internal/BamToolsIndex_p.h +++ b/src/api/internal/BamToolsIndex_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamToolsIndex.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp index 8f1b167..c9199b9 100644 --- a/src/api/internal/BamWriter_p.cpp +++ b/src/api/internal/BamWriter_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BamWriter_p.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 16 June 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/BamWriter_p.h index dd2b0fe..caa440e 100644 --- a/src/api/internal/BamWriter_p.h +++ b/src/api/internal/BamWriter_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BamWriter_p.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 24 February 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BgzfStream_p.cpp b/src/api/internal/BgzfStream_p.cpp index 4db9b15..3b70749 100644 --- a/src/api/internal/BgzfStream_p.cpp +++ b/src/api/internal/BgzfStream_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // BgzfStream_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 9 September 2011(DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h index 04b6c34..f7ea268 100644 --- a/src/api/internal/BgzfStream_p.h +++ b/src/api/internal/BgzfStream_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // BgzfStream_p.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 5 April 2011(DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamFormatParser_p.cpp b/src/api/internal/SamFormatParser_p.cpp index 316f75f..1431b7a 100644 --- a/src/api/internal/SamFormatParser_p.cpp +++ b/src/api/internal/SamFormatParser_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamFormatParser.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamFormatParser_p.h b/src/api/internal/SamFormatParser_p.h index daabe39..cf6d54c 100644 --- a/src/api/internal/SamFormatParser_p.h +++ b/src/api/internal/SamFormatParser_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamFormatParser.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 23 December 2010 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp index 1e670b0..df13fe5 100644 --- a/src/api/internal/SamFormatPrinter_p.cpp +++ b/src/api/internal/SamFormatPrinter_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamFormatPrinter.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamFormatPrinter_p.h b/src/api/internal/SamFormatPrinter_p.h index 5e28e97..8250db6 100644 --- a/src/api/internal/SamFormatPrinter_p.h +++ b/src/api/internal/SamFormatPrinter_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamFormatPrinter.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 23 December 2010 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/SamHeaderValidator_p.cpp index 7ecec2c..936da49 100644 --- a/src/api/internal/SamHeaderValidator_p.cpp +++ b/src/api/internal/SamHeaderValidator_p.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // SamHeaderValidator.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamHeaderValidator_p.h b/src/api/internal/SamHeaderValidator_p.h index 06a82ab..1fc1644 100644 --- a/src/api/internal/SamHeaderValidator_p.h +++ b/src/api/internal/SamHeaderValidator_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamHeaderValidator.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 13 January 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/api/internal/SamHeaderVersion_p.h b/src/api/internal/SamHeaderVersion_p.h index 2564017..d166ca2 100644 --- a/src/api/internal/SamHeaderVersion_p.h +++ b/src/api/internal/SamHeaderVersion_p.h @@ -1,7 +1,6 @@ // *************************************************************************** // SamHeaderVersion.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 24 February 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/shared/bamtools_global.h b/src/shared/bamtools_global.h index 6380bb0..1b2a8af 100644 --- a/src/shared/bamtools_global.h +++ b/src/shared/bamtools_global.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_global.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 3 March 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp index 1230e04..97c032f 100644 --- a/src/toolkit/bamtools.cpp +++ b/src/toolkit/bamtools.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 May 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp index f3bc486..991cebc 100644 --- a/src/toolkit/bamtools_convert.cpp +++ b/src/toolkit/bamtools_convert.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 11 June 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_convert.h b/src/toolkit/bamtools_convert.h index 8dd6857..9cc3b89 100644 --- a/src/toolkit/bamtools_convert.h +++ b/src/toolkit/bamtools_convert.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_convert.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 9 July 2010 // --------------------------------------------------------------------------- @@ -35,4 +34,4 @@ class ConvertTool : public AbstractTool { } // namespace BamTools -#endif // BAMTOOLS_CONVERT_H \ No newline at end of file +#endif // BAMTOOLS_CONVERT_H diff --git a/src/toolkit/bamtools_count.cpp b/src/toolkit/bamtools_count.cpp index c17b257..3c46f67 100644 --- a/src/toolkit/bamtools_count.cpp +++ b/src/toolkit/bamtools_count.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_count.h b/src/toolkit/bamtools_count.h index d9c3c3d..553f9b0 100644 --- a/src/toolkit/bamtools_count.h +++ b/src/toolkit/bamtools_count.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp index c3eaa20..c0ecd8f 100644 --- a/src/toolkit/bamtools_coverage.cpp +++ b/src/toolkit/bamtools_coverage.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_coverage.h b/src/toolkit/bamtools_coverage.h index e9e8a71..a542ec2 100644 --- a/src/toolkit/bamtools_coverage.h +++ b/src/toolkit/bamtools_coverage.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_coverage.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 1 August 2010 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp index 9ea3660..baf2816 100644 --- a/src/toolkit/bamtools_filter.cpp +++ b/src/toolkit/bamtools_filter.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_filter.h b/src/toolkit/bamtools_filter.h index 4d125c9..7fa5f73 100644 --- a/src/toolkit/bamtools_filter.h +++ b/src/toolkit/bamtools_filter.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_filter.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 28 August 2010 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_header.cpp b/src/toolkit/bamtools_header.cpp index 984ddd4..a08c632 100644 --- a/src/toolkit/bamtools_header.cpp +++ b/src/toolkit/bamtools_header.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_header.h b/src/toolkit/bamtools_header.h index 7b5f100..7e59d68 100644 --- a/src/toolkit/bamtools_header.h +++ b/src/toolkit/bamtools_header.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_header.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_index.cpp b/src/toolkit/bamtools_index.cpp index c1bd2e5..ef0e765 100644 --- a/src/toolkit/bamtools_index.cpp +++ b/src/toolkit/bamtools_index.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_index.h b/src/toolkit/bamtools_index.h index 11cc057..a670741 100644 --- a/src/toolkit/bamtools_index.h +++ b/src/toolkit/bamtools_index.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_index.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_merge.cpp b/src/toolkit/bamtools_merge.cpp index 7cfc099..1e8312f 100644 --- a/src/toolkit/bamtools_merge.cpp +++ b/src/toolkit/bamtools_merge.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_merge.h b/src/toolkit/bamtools_merge.h index b1c2e1f..cab851c 100644 --- a/src/toolkit/bamtools_merge.h +++ b/src/toolkit/bamtools_merge.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_merge.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_random.cpp b/src/toolkit/bamtools_random.cpp index 927349e..e28ea70 100644 --- a/src/toolkit/bamtools_random.cpp +++ b/src/toolkit/bamtools_random.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_random.h b/src/toolkit/bamtools_random.h index 688ab5c..ce70b86 100644 --- a/src/toolkit/bamtools_random.h +++ b/src/toolkit/bamtools_random.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_random.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2010 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_resolve.cpp b/src/toolkit/bamtools_resolve.cpp index 8be405f..9a1a3b0 100644 --- a/src/toolkit/bamtools_resolve.cpp +++ b/src/toolkit/bamtools_resolve.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_resolve.cpp (c) 2011 // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 6 July 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_resolve.h b/src/toolkit/bamtools_resolve.h index 681a557..f90dec0 100644 --- a/src/toolkit/bamtools_resolve.h +++ b/src/toolkit/bamtools_resolve.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_resolve.h (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 23 June 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_revert.cpp b/src/toolkit/bamtools_revert.cpp index c751ce4..ba0debe 100644 --- a/src/toolkit/bamtools_revert.cpp +++ b/src/toolkit/bamtools_revert.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_revert.cpp (c) 2010 Derek Barnett, Alistair Ward // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_revert.h b/src/toolkit/bamtools_revert.h index 4b2a24c..7aa270d 100644 --- a/src/toolkit/bamtools_revert.h +++ b/src/toolkit/bamtools_revert.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_revert.h (c) 2010 Derek Barnett, Alistair Ward // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp index dd6d951..fb181a8 100644 --- a/src/toolkit/bamtools_sort.cpp +++ b/src/toolkit/bamtools_sort.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 14 June 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_sort.h b/src/toolkit/bamtools_sort.h index fe0ed5d..d746f5e 100644 --- a/src/toolkit/bamtools_sort.h +++ b/src/toolkit/bamtools_sort.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_sort.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_split.cpp b/src/toolkit/bamtools_split.cpp index bfbf303..4575d85 100644 --- a/src/toolkit/bamtools_split.cpp +++ b/src/toolkit/bamtools_split.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_split.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_split.h b/src/toolkit/bamtools_split.h index 776037c..a294f4f 100644 --- a/src/toolkit/bamtools_split.h +++ b/src/toolkit/bamtools_split.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_split.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 (DB) // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_stats.cpp b/src/toolkit/bamtools_stats.cpp index f66c462..eb57a95 100644 --- a/src/toolkit/bamtools_stats.cpp +++ b/src/toolkit/bamtools_stats.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_stats.h b/src/toolkit/bamtools_stats.h index 799befe..29cc998 100644 --- a/src/toolkit/bamtools_stats.h +++ b/src/toolkit/bamtools_stats.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_stats.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 7 April 2011 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_tool.h b/src/toolkit/bamtools_tool.h index 816c8c5..f14d460 100644 --- a/src/toolkit/bamtools_tool.h +++ b/src/toolkit/bamtools_tool.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_tool.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 2 June 2010 // --------------------------------------------------------------------------- diff --git a/src/toolkit/bamtools_version.h.in b/src/toolkit/bamtools_version.h.in index aa7c06a..325314c 100644 --- a/src/toolkit/bamtools_version.h.in +++ b/src/toolkit/bamtools_version.h.in @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_version.h.in (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 (DB) // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp index f6434d3..2e7a784 100644 --- a/src/utils/bamtools_fasta.cpp +++ b/src/utils/bamtools_fasta.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_fasta.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 13 July 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h index d0ae8e4..5cf85b3 100644 --- a/src/utils/bamtools_fasta.h +++ b/src/utils/bamtools_fasta.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_filter_engine.h b/src/utils/bamtools_filter_engine.h index 9ea1e8d..ae1415d 100644 --- a/src/utils/bamtools_filter_engine.h +++ b/src/utils/bamtools_filter_engine.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_filter_engine.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_filter_properties.h b/src/utils/bamtools_filter_properties.h index 9de3e27..c810ba2 100644 --- a/src/utils/bamtools_filter_properties.h +++ b/src/utils/bamtools_filter_properties.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_filter_properties.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_filter_ruleparser.h b/src/utils/bamtools_filter_ruleparser.h index 3ad2bfa..07328cb 100644 --- a/src/utils/bamtools_filter_ruleparser.h +++ b/src/utils/bamtools_filter_ruleparser.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_filter_ruleparser.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_options.cpp b/src/utils/bamtools_options.cpp index 157357f..359018b 100644 --- a/src/utils/bamtools_options.cpp +++ b/src/utils/bamtools_options.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_options.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 11 June 2011 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_options.h b/src/utils/bamtools_options.h index 98ddc3d..b49fd53 100644 --- a/src/utils/bamtools_options.h +++ b/src/utils/bamtools_options.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 11 June 2011 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_pileup_engine.cpp b/src/utils/bamtools_pileup_engine.cpp index bc0e7c8..e0a0ea9 100644 --- a/src/utils/bamtools_pileup_engine.cpp +++ b/src/utils/bamtools_pileup_engine.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_pileup_engine.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_pileup_engine.h b/src/utils/bamtools_pileup_engine.h index 6900dc9..24d7084 100644 --- a/src/utils/bamtools_pileup_engine.h +++ b/src/utils/bamtools_pileup_engine.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 18 September 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_utilities.cpp b/src/utils/bamtools_utilities.cpp index 1d5e00d..f79faac 100644 --- a/src/utils/bamtools_utilities.cpp +++ b/src/utils/bamtools_utilities.cpp @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_utilities.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 9 June 2011 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h index 71d4683..d9a3192 100644 --- a/src/utils/bamtools_utilities.h +++ b/src/utils/bamtools_utilities.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 8 September 2011 // --------------------------------------------------------------------------- diff --git a/src/utils/bamtools_variant.h b/src/utils/bamtools_variant.h index 116a2c0..020b336 100644 --- a/src/utils/bamtools_variant.h +++ b/src/utils/bamtools_variant.h @@ -1,7 +1,6 @@ // *************************************************************************** // bamtools_variant.h (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 // --------------------------------------------------------------------------- diff --git a/src/utils/utils_global.h b/src/utils/utils_global.h index 8aa2826..c793e8c 100644 --- a/src/utils/utils_global.h +++ b/src/utils/utils_global.h @@ -1,7 +1,6 @@ // *************************************************************************** // utils_global.h (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- // Last modified: 19 November 2010 (DB) // ---------------------------------------------------------------------------