merge conflict

[bamtools.git] / src / api / BamMultiReader.h

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index 561ce7a1e4d4407e2c85975b3a2ab2cd455a5ee3..959048c27f1f6dea1ee5fc5522abd53ea019fb90 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -2,7 +2,7 @@
 // BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 15 March 2011 (DB)
+// Last modified: 1 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Convenience class for reading multiple BAM files.
 // ***************************************************************************
@@ -25,12 +25,6 @@ namespace Internal {
 
 class API_EXPORT BamMultiReader {
 
-    public:
-        enum SortOrder { SortedByPosition = 0
-                       , SortedByReadName
-                       , Unsorted
-                       };
-
     // constructor / destructor
     public:
         BamMultiReader(void);
@@ -73,12 +67,9 @@ class API_EXPORT BamMultiReader {
 
         // retrieves next available alignment
         bool GetNextAlignment(BamAlignment& alignment);
-        // retrieves next available alignmnet (without populating the alignment's string data fields)
+        // retrieves next available alignment (without populating the alignment's string data fields)
         bool GetNextAlignmentCore(BamAlignment& alignment);
 
-        // sets the expected sorting order for reading across multiple BAM files
-        void SetSortOrder(const SortOrder& order);
-
         // ----------------------
         // access auxiliary data
         // ----------------------
@@ -109,13 +100,6 @@ class API_EXPORT BamMultiReader {
         // changes the caching behavior of the index data
         void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
 
-    // deprecated methods
-    public:
-        // returns \c true if all BAM files have index data available.
-        bool IsIndexLoaded(void) const;
-        // convenience method for printing filenames to stdout
-        void PrintFilenames(void) const;
-
     // private implementation
     private:
         Internal::BamMultiReaderPrivate* d;