Added UNSORTED to BamMultiReader::SortOrder types. Unsorted BAMs are 'merged' through...

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index 6de73731d81b71bb349704af88bddb09a9caa7af..cc36efc42309166728674f701d8743094119e5c9 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 23 December 2010 (DB)\r
+// Last modified: 17 January 2011 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Functionality for simultaneously reading multiple BAM files\r
 // ***************************************************************************\r
@@ -82,7 +82,10 @@ class API_EXPORT BamMultiReader {
         bool HasOpenReaders(void);\r
         // set sort order for merging BAM files (i.e. which alignment from the files is 'next'?)\r
         // default behavior is to sort by position, use this method to handle BAMs sorted by read name\r
-        enum SortOrder { SortedByPosition = 0, SortedByReadName};\r
+        enum SortOrder { SortedByPosition = 0\r
+                       , SortedByReadName\r
+                       , Unsorted\r
+                       };\r
         void SetSortOrder(const SortOrder& order);\r
 \r
         // ----------------------\r

diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h
index 5d1e058747bfa004ea43f77f17c7e3b1dcb04e24..c9d1286534185b9ea0cd47c5c956def6d11fc45d 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: 19 November 2010 (DB)
+// Last modified: 17 January 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides merging functionality for BamMultiReader.  At this point, supports
 // sorting results by (refId, position) or by read name.
@@ -25,6 +25,7 @@
 #include <api/BamAlignment.h>
 #include <api/BamReader.h>
 #include <map>
+#include <queue>
 #include <string>
 #include <utility>
 
@@ -96,6 +97,25 @@ class ReadNameMultiMerger : public IBamMultiMerger {
         IndexType m_data;
 };
 
+// IBamMultiMerger implementation - unsorted BAM file(s)
+class UnsortedMultiMerger : public IBamMultiMerger {
+
+    public:
+        UnsortedMultiMerger(void) : IBamMultiMerger() { }
+        ~UnsortedMultiMerger(void) { }
+
+    public:
+        void Add(const ReaderAlignment& value);
+        void Clear(void);
+        const ReaderAlignment& First(void) const;
+        const int Size(void) const;
+        ReaderAlignment TakeFirst(void);
+
+    private:
+        typedef std::queue<ReaderAlignment> IndexType;
+        IndexType m_data;
+};
+
 // ------------------------------------------
 // PositionMultiMerger implementation
 
@@ -152,6 +172,31 @@ inline ReaderAlignment ReadNameMultiMerger::TakeFirst(void) {
     return next;
 }
 
+// ------------------------------------------
+// UnsortedMultiMerger implementation
+
+inline void UnsortedMultiMerger::Add(const ReaderAlignment& value) {
+    m_data.push(value);
+}
+
+inline void UnsortedMultiMerger::Clear(void) {
+    m_data.clear();
+}
+
+inline const ReaderAlignment& UnsortedMultiMerger::First(void) const {
+    return m_data.front();
+}
+
+inline const int UnsortedMultiMerger::Size(void) const {
+    return m_data.size();
+}
+
+inline ReaderAlignment UnsortedMultiMerger::TakeFirst(void) {
+    ReaderAlignment first = m_data.front();
+    m_data.pop();
+    return first;
+}
+
 } // namespace Internal
 } // namespace BamTools
 

diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp
index 01cdf8f9d2c38a8a5d40946c3897424bfc045e63..bfec6bbf2581cdf674e7f3386cb0a30462df899b 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: 23 December 2010 (DB)
+// Last modified: 17 January 2011 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -26,7 +26,7 @@ using namespace std;
 BamMultiReaderPrivate::BamMultiReaderPrivate(void)
     : m_alignments(0)
     , m_isCoreMode(false)
-    , m_isSortedByPosition(true)
+    , m_sortOrder(BamMultiReader::SortedByPosition)
 { }
 
 // dtor
@@ -66,9 +66,9 @@ void BamMultiReaderPrivate::Close(void) {
     // clear out readers
     m_readers.clear();
 
-    // reset flags
+    // reset default flags
     m_isCoreMode = false;
-    m_isSortedByPosition = true;
+    m_sortOrder = BamMultiReader::SortedByPosition;
 }
 
 // saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
@@ -84,6 +84,16 @@ bool BamMultiReaderPrivate::CreateIndexes(bool useStandardIndex) {
     return result;
 }
 
+IBamMultiMerger* BamMultiReaderPrivate::CreateMergerForCurrentSortOrder(void) const {
+    switch ( m_sortOrder ) {
+        case ( BamMultiReader::SortedByPosition ) : return new PositionMultiMerger;
+        case ( BamMultiReader::SortedByReadName ) : return new ReadNameMultiMerger;
+        case ( BamMultiReader::Unsorted )         : return new UnsortedMultiMerger;
+        default : //print error
+            return 0;
+    }
+}
+
 const string BamMultiReaderPrivate::ExtractReadGroup(const string& headerLine) const {
 
     string readGroup("");
@@ -305,10 +315,8 @@ bool BamMultiReaderPrivate::Open(const vector<string>& filenames,
     }
 
     // create alignment cache based on sorting mode
-    if ( m_isSortedByPosition )
-        m_alignments = new PositionMultiMerger;
-    else
-        m_alignments = new ReadNameMultiMerger;
+    m_alignments = CreateMergerForCurrentSortOrder();
+    if ( m_alignments == 0 ) return false;
 
     // iterate over filenames
     vector<string>::const_iterator filenameIter = filenames.begin();
@@ -382,8 +390,8 @@ bool BamMultiReaderPrivate::Rewind(void) {
 
 void BamMultiReaderPrivate::SaveNextAlignment(BamReader* reader, BamAlignment* alignment) {
 
-    // must be in core mode && sorting by position to call GNACore()
-    if ( m_isCoreMode && m_isSortedByPosition ) {
+    // 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) );
     }
@@ -432,21 +440,15 @@ bool BamMultiReaderPrivate::SetRegion(const BamRegion& region) {
 
 void BamMultiReaderPrivate::SetSortOrder(const BamMultiReader::SortOrder& order) {
 
-    const BamMultiReader::SortOrder oldSortOrder = ( m_isSortedByPosition ? BamMultiReader::SortedByPosition
-                                                                          : BamMultiReader::SortedByReadName ) ;
     // skip if no change needed
-    if ( oldSortOrder == order ) return;
+    if ( m_sortOrder == order ) return;
 
-    // create new alignment cache
-    IBamMultiMerger* newAlignmentCache(0);
-    if ( order == BamMultiReader::SortedByPosition ) {
-        newAlignmentCache = new PositionMultiMerger;
-        m_isSortedByPosition = true;
-    }
-    else {
-        newAlignmentCache = new ReadNameMultiMerger;
-        m_isSortedByPosition = false;
-    }
+    // set new sort order
+    m_sortOrder = order;
+
+    // create new alignment cache based on sort order
+    IBamMultiMerger* newAlignmentCache = CreateMergerForCurrentSortOrder();
+    if ( newAlignmentCache == 0 ) return; // print error?
 
     // copy old cache contents to new cache
     while ( m_alignments->Size() > 0 ) {

diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
index 971acda2a0008869de2f879bb175dfe2945cc0fd..942f60b3da6d3835435eb81735002e94029ba243 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: 23 December 2010 (DB)
+// Last modified: 17 January 2011 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -70,6 +70,7 @@ class BamMultiReaderPrivate {
 
     // internal methods
     private:
+        IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const;
         const std::string ExtractReadGroup(const std::string& headerLine) const;
         bool LoadNextAlignment(BamAlignment& al, bool coreMode);
         void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment);
@@ -86,10 +87,10 @@ class BamMultiReaderPrivate {
 
         IBamMultiMerger* m_alignments;
         bool m_isCoreMode;
-        bool m_isSortedByPosition;
+        BamMultiReader::SortOrder m_sortOrder;
 };
 
-} // namesapce Internal
+} // namespace Internal
 } // namespace BamTools
 
 #endif // BAMMULTIREADER_P_H