Removed 'core mode' concept from BamMultiReader internals

 * Now char data is only generated if needed by multi-merger
implementation or on-demand by client call to
BamMultiReader::GetNextAlignment()

diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h
index ae67eea238df983b4e8968b41414ef1c5abd5fcc..51e5d38b236c7f1d0c32730702657776d5df875c 100644 (file)
--- a/src/api/internal/BamMultiMerger_p.h
+++ b/src/api/internal/BamMultiMerger_p.h
@@ -3,7 +3,7 @@
 // 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 +42,7 @@ 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 +59,7 @@ 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 +87,7 @@ 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 +115,7 @@ 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 +135,7 @@ 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 +188,12 @@ 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 +245,7 @@ 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 e789d06ee35c93d3945427ec99a4fe544af49930..9776f884e0fbcece6411f706903742b7736ae175 100644 (file)
--- a/src/api/internal/BamMultiReader_p.cpp
+++ b/src/api/internal/BamMultiReader_p.cpp
@@ -3,7 +3,7 @@
 // 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 +25,6 @@ using namespace std;
 // ctor
 BamMultiReaderPrivate::BamMultiReaderPrivate(void)
     : m_alignments(0)
-    , m_isCoreMode(false)
     , m_sortOrder(BamMultiReader::SortedByPosition)
 { }
 
@@ -261,14 +260,12 @@ 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 +403,10 @@ 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
@@ -566,6 +548,33 @@ 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 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;
+
+    // set char data if requested
+    if ( needCharData ) {
+        al.BuildCharData();
+        al.Filename = reader->GetFilename();
+    }
+
+    // peek to next alignment & 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 +613,9 @@ 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 +704,6 @@ 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<ReaderAlignment>::iterator readerIter = m_readers.begin();
     vector<ReaderAlignment>::iterator readerEnd  = m_readers.end();

diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
index b34fb0c583eb016167846d2cf937e14cab669c01..85c5b85aa43b40b742ee60ce1c1ad9e6835ee78b 100644 (file)
--- a/src/api/internal/BamMultiReader_p.h
+++ b/src/api/internal/BamMultiReader_p.h
@@ -3,7 +3,7 @@
 // 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
 // *************************************************************************
@@ -78,10 +78,11 @@ 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);
+        BamReader* OpenReader(const std::string& filename);
+        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<std::string> SplitHeaderText(const std::string& headerText) const;
         void UpdateAlignmentCache(void);
         void ValidateReaders(void) const;
@@ -92,7 +93,6 @@ class BamMultiReaderPrivate {
         std::vector<ReaderAlignment> m_readers;
 
         IBamMultiMerger* m_alignments;
-        bool m_isCoreMode;
         BamMultiReader::SortOrder m_sortOrder;
 };