Added explicit merge order to BamMultiReader

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

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index 561ce7a1e4d4407e2c85975b3a2ab2cd455a5ee3..27745628cb0f0dabf3c819d2eb659b15aca5a33b 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: 14 January 2013 (DB)
 // ---------------------------------------------------------------------------
 // Convenience class for reading multiple BAM files.
 // ***************************************************************************
@@ -10,8 +10,8 @@
 #ifndef BAMMULTIREADER_H
 #define BAMMULTIREADER_H
 
-#include <api/api_global.h>
-#include <api/BamReader.h>
+#include "api/api_global.h"
+#include "api/BamReader.h"
 #include <map>
 #include <sstream>
 #include <string>
@@ -25,11 +25,13 @@ namespace Internal {
 
 class API_EXPORT BamMultiReader {
 
+    // enums
     public:
-        enum SortOrder { SortedByPosition = 0
-                       , SortedByReadName
-                       , Unsorted
-                       };
+        // possible merge order strategies
+        enum MergeOrder { RoundRobinMerge = 0
+                        , MergeByCoordinate
+                        , MergeByName
+                        };
 
     // constructor / destructor
     public:
@@ -44,11 +46,13 @@ class API_EXPORT BamMultiReader {
         // ----------------------
 
         // closes all open BAM files
-        void Close(void);
+        bool Close(void);
         // close only the requested BAM file
-        void CloseFile(const std::string& filename);
+        bool CloseFile(const std::string& filename);
         // returns list of filenames for all open BAM files
         const std::vector<std::string> Filenames(void) const;
+        // returns curent merge order strategy
+        BamMultiReader::MergeOrder GetMergeOrder(void) const;
         // returns true if multireader has any open BAM files
         bool HasOpenReaders(void) const;
         // performs random-access jump within current BAM files
@@ -59,6 +63,8 @@ class API_EXPORT BamMultiReader {
         bool OpenFile(const std::string& filename);
         // returns file pointers to beginning of alignments
         bool Rewind(void);
+        // sets an explicit merge order, regardless of the BAM files' SO header tag
+        void SetExplicitMergeOrder(BamMultiReader::MergeOrder order);
         // sets the target region of interest
         bool SetRegion(const BamRegion& region);
         // sets the target region of interest
@@ -73,12 +79,9 @@ 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
         // ----------------------
@@ -106,15 +109,13 @@ class API_EXPORT BamMultiReader {
         bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
         // opens index files for current BAM files.
         bool OpenIndexes(const std::vector<std::string>& indexFilenames);
-        // 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;
+        // ----------------------
+        // error handling
+        // ----------------------
+
+        // returns a human-readable description of the last error that occurred
+        std::string GetErrorString(void) const;
 
     // private implementation
     private: