Organized api/internal into subdirs

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

diff --git a/src/api/internal/bam/BamMultiReader_p.h b/src/api/internal/bam/BamMultiReader_p.h
new file mode 100644 (file)
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+++ b/src/api/internal/bam/BamMultiReader_p.h
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+// ***************************************************************************
+// BamMultiReader_p.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 25 October 2011 (DB)
+// ---------------------------------------------------------------------------
+// Functionality for simultaneously reading multiple BAM files
+// *************************************************************************
+
+#ifndef BAMMULTIREADER_P_H
+#define BAMMULTIREADER_P_H
+
+//  -------------
+//  W A R N I N G
+//  -------------
+//
+// This file is not part of the BamTools API.  It exists purely as an
+// implementation detail. This header file may change from version to version
+// without notice, or even be removed.
+//
+// We mean it.
+
+#include "api/SamHeader.h"
+#include "api/BamMultiReader.h"
+#include "api/internal/bam/BamMultiMerger_p.h"
+#include <string>
+#include <vector>
+
+namespace BamTools {
+namespace Internal {
+
+class BamMultiReaderPrivate {
+
+    // typedefs
+    public:
+        typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+
+    // constructor / destructor
+    public:
+        BamMultiReaderPrivate(void);
+        ~BamMultiReaderPrivate(void);
+
+    // public interface
+    public:
+
+        // file operations
+        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);
+        bool OpenFile(const std::string& filename);
+        bool Rewind(void);
+        bool SetRegion(const BamRegion& region);
+
+        // access alignment data
+        bool GetNextAlignment(BamAlignment& al);
+        bool GetNextAlignmentCore(BamAlignment& al);
+        bool HasOpenReaders(void);
+
+        // access auxiliary data
+        SamHeader GetHeader(void) const;
+        std::string GetHeaderText(void) const;
+        int GetReferenceCount(void) const;
+        const BamTools::RefVector GetReferenceData(void) const;
+        int GetReferenceID(const std::string& refName) const;
+
+        // BAM index operations
+        bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD);
+        bool HasIndexes(void) const;
+        bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
+        bool OpenIndexes(const std::vector<std::string>& indexFilenames);
+
+        // 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;
+
+    // data members
+    public:
+        std::vector<MergeItem> m_readers;
+        IMultiMerger* m_alignmentCache;
+        mutable std::string m_errorString;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMMULTIREADER_P_H