Removed 'core mode' concept from BamMultiReader internals

[bamtools.git] / src / api / internal / BamMultiReader_p.h

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;
 };