Removed index cache mode

[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 70640a3fede57e9e3fa9656a21b4cfa83d9e47ef..9d001f5be0dfd401651e49282960966a49db59b6 100644 (file)
--- a/src/api/internal/BamMultiReader_p.h
+++ b/src/api/internal/BamMultiReader_p.h
@@ -2,7 +2,7 @@
 // BamMultiReader_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 3 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -20,9 +20,9 @@
 //
 // We mean it.
 
-#include <api/SamHeader.h>
-#include <api/BamMultiReader.h>
-#include <api/internal/BamMultiMerger_p.h>
+#include "api/SamHeader.h"
+#include "api/BamMultiReader.h"
+#include "api/internal/BamMultiMerger_p.h"
 #include <string>
 #include <vector>
 
@@ -31,6 +31,10 @@ namespace Internal {
 
 class BamMultiReaderPrivate {
 
+    // typedefs
+    public:
+        typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+
     // constructor / destructor
     public:
         BamMultiReaderPrivate(void);
@@ -40,9 +44,8 @@ class BamMultiReaderPrivate {
     public:
 
         // file operations
-        void Close(void);
-        void CloseFile(const std::string& filename);
-        void CloseFiles(const std::vector<std::string>& filenames);
+        bool Close(void);
+        bool CloseFile(const std::string& filename);
         const std::vector<std::string> Filenames(void) const;
         bool Jump(int refID, int position = 0);
         bool Open(const std::vector<std::string>& filenames);
@@ -67,14 +70,19 @@ class BamMultiReaderPrivate {
         bool HasIndexes(void) const;
         bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
         bool OpenIndexes(const std::vector<std::string>& indexFilenames);
-        void SetIndexCacheMode(const BamIndex::IndexCacheMode mode);
+
+        // error handling
+        std::string GetErrorString(void) const;
 
     // 'internal' methods
     public:
+
+        bool CloseFiles(const std::vector<std::string>& filenames);
         IMultiMerger* CreateAlignmentCache(void) const;
         bool PopNextCachedAlignment(BamAlignment& al, const bool needCharData);
         bool RewindReaders(void);
         void SaveNextAlignment(BamReader* reader, BamAlignment* alignment);
+        void SetErrorString(const std::string& where, const std::string& what) const; //
         bool UpdateAlignmentCache(void);
         bool ValidateReaders(void) const;
 
@@ -82,6 +90,7 @@ class BamMultiReaderPrivate {
     public:
         std::vector<MergeItem> m_readers;
         IMultiMerger* m_alignmentCache;
+        mutable std::string m_errorString;
 };
 
 } // namespace Internal