X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamReader.h;h=15b41354d9e2e119e2c1e4e2cc38cd80fd500ecc;hb=e9977c58d60d1a1b2034eb3f01cd0183cbfe8736;hp=ce04af65a9edbd364c323dba22acde565dd3ea0c;hpb=8a90b7aefffaf186053ef4da96c8663bf528274a;p=bamtools.git

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index ce04af6..15b4135 100644
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -2,7 +2,7 @@
 // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 18 November 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides read access to BAM files.
 // ***************************************************************************
@@ -10,10 +10,10 @@
 #ifndef BAMREADER_H
 #define BAMREADER_H
 
-#include <api/api_global.h>
-#include <api/BamAlignment.h>
-#include <api/BamIndex.h>
-#include <api/SamHeader.h>
+#include "api/api_global.h"
+#include "api/BamAlignment.h"
+#include "api/BamIndex.h"
+#include "api/SamHeader.h"
 #include <string>
 
 namespace BamTools {
@@ -69,7 +69,9 @@ class API_EXPORT BamReader {
         // access header data
         // ----------------------
 
-        // returns SAM header data
+        // returns a read-only reference to SAM header data
+        const SamHeader& GetConstSamHeader(void) const;
+        // returns an editable copy of SAM header data
         SamHeader GetHeader(void) const;
         // returns SAM header data, as SAM-formatted text
         std::string GetHeaderText(void) const;
@@ -99,8 +101,6 @@ class API_EXPORT BamReader {
         bool OpenIndex(const std::string& indexFilename);
         // sets a custom BamIndex on this reader
         void SetIndex(BamIndex* index);
-        // changes the caching behavior of the index data
-        void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
 
         // ----------------------
         // error handling
@@ -108,11 +108,6 @@ class API_EXPORT BamReader {
 
         // returns a human-readable description of the last error that occurred
         std::string GetErrorString(void) const;
-
-    // deprecated methods
-    public:
-        // returns true if index data is available
-        bool IsIndexLoaded(void) const;
         
     // private implementation
     private: