Implemented proper -byname sorting (finally).

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

diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
new file mode 100644 (file)
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--- /dev/null
+++ b/src/api/internal/BamMultiReader_p.h
@@ -0,0 +1,95 @@
+// ***************************************************************************
+// BamMultiReader_p.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (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/BamMultiReader.h>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+namespace Internal {
+
+class IBamMultiMerger;
+
+class BamMultiReaderPrivate {
+
+    // constructor / destructor
+    public:
+        BamMultiReaderPrivate(void);
+        ~BamMultiReaderPrivate(void);
+
+    // public interface
+    public:
+
+        // file operations
+        void Close(void);
+        bool Open(const std::vector<std::string>& filenames,
+                  bool openIndexes = true,
+                  bool coreMode = false,
+                  bool preferStandardIndex = false);
+        bool IsIndexLoaded(void) const;
+        bool Jump(int refID, int position = 0);
+        void PrintFilenames(void) const;
+        bool SetRegion(const BamRegion& region);
+        bool Rewind(void);
+
+        // access alignment data
+        bool GetNextAlignment(BamAlignment& al);
+        bool GetNextAlignmentCore(BamAlignment& al);
+        bool HasOpenReaders(void);
+        void SetSortOrder(const BamMultiReader::SortOrder& order);
+
+        // access auxiliary data
+        const std::string GetHeaderText(void) const;
+        const int GetReferenceCount(void) const;
+        const BamTools::RefVector GetReferenceData(void) const;
+        const int GetReferenceID(const std::string& refName) const;
+
+        // BAM index operations
+        bool CreateIndexes(bool useStandardIndex = true);
+        void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
+
+    // internal methods
+    private:
+        const std::string ExtractReadGroup(const std::string& headerLine) const;
+        bool LoadNextAlignment(BamAlignment& al, bool coreMode);
+        void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment);
+        const std::vector<std::string> SplitHeaderText(const std::string& headerText) const;
+        // updates our alignment cache
+        void UpdateAlignments(void);
+        // validates that we have a congruent set of BAM files that are aligned against the same reference sequences
+        void ValidateReaders(void) const;
+
+    // data members
+    public:
+        typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+        std::vector<ReaderAlignment> m_readers;
+
+        IBamMultiMerger* m_alignments;
+        bool m_isCoreMode;
+        bool m_isSortedByPosition;
+};
+
+} // namesapce Internal
+} // namespace BamTools
+
+#endif // BAMMULTIREADER_P_H