diff spp/src/BamMultiReader.h @ 6:ce08b0efa3fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamMultiReader.h	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,136 @@
+// ***************************************************************************
+// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Functionality for simultaneously reading multiple BAM files
+// ***************************************************************************
+
+#ifndef BAMMULTIREADER_H
+#define BAMMULTIREADER_H
+
+#include <api_global.h>
+#include <BamReader.h>
+#include <map>
+#include <sstream>
+#include <string>
+#include <utility>
+
+namespace BamTools {
+
+// index mapping reference/position pairings to bamreaders and their alignments
+typedef std::multimap<std::pair<int, int>, std::pair<BamReader*, BamAlignment*> > AlignmentIndex;
+
+class API_EXPORT BamMultiReader {
+
+    // constructor / destructor
+    public:
+        BamMultiReader(void);
+        ~BamMultiReader(void);
+
+    // public interface
+    public:
+
+        // positioning
+        int CurrentRefID;
+        int CurrentLeft;
+
+        // region under analysis, specified using SetRegion
+        BamRegion Region;
+
+        // ----------------------
+        // BAM file operations
+        // ----------------------
+
+        // close BAM files
+        void Close(void);
+
+        // opens BAM files (and optional BAM index files, if provided)
+        // @openIndexes - triggers index opening, useful for suppressing
+        // error messages during merging of files in which we may not have
+        // indexes.
+        // @coreMode - setup our first alignments using GetNextAlignmentCore();
+        // also useful for merging
+        // @preferStandardIndex - look for standard BAM index ".bai" first.  If false, 
+        // will look for BamTools index ".bti".  
+        bool Open(const std::vector<std::string>& filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = false);
+
+        // returns whether underlying BAM readers ALL have an index loaded
+        // this is useful to indicate whether Jump() or SetRegion() are possible
+        bool IsIndexLoaded(void) const;
+        
+        // performs random-access jump to reference, position
+        bool Jump(int refID, int position = 0);
+
+        // sets the target region
+        bool SetRegion(const BamRegion& region);
+        bool SetRegion(const int&, const int&, const int&, const int&); // convenience function to above
+
+        // returns file pointers to beginning of alignments
+        bool Rewind(void);
+
+        // ----------------------
+        // access alignment data
+        // ----------------------
+        // updates the reference id marker to match the lower limit of our readers
+        void UpdateReferenceID(void);
+
+        // retrieves next available alignment (returns success/fail) from all files
+        bool GetNextAlignment(BamAlignment&);
+        // retrieves next available alignment (returns success/fail) from all files
+        // and populates the support data with information about the alignment
+        // *** BUT DOES NOT PARSE CHARACTER DATA FROM THE ALIGNMENT
+        bool GetNextAlignmentCore(BamAlignment&);
+        // ... should this be private?
+        bool HasOpenReaders(void);
+
+        // ----------------------
+        // access auxiliary data
+        // ----------------------
+
+        // returns unified SAM header text for all files
+        const std::string GetHeaderText(void) const;
+        // returns number of reference sequences
+        const int GetReferenceCount(void) const;
+        // returns vector of reference objects
+        const BamTools::RefVector GetReferenceData(void) const;
+        // returns reference id (used for BamMultiReader::Jump()) for the given reference name
+        const int GetReferenceID(const std::string& refName) const;
+        // validates that we have a congruent set of BAM files that are aligned against the same reference sequences
+        void ValidateReaders() const;
+
+        // ----------------------
+        // BAM index operations
+        // ----------------------
+
+        // creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")
+        bool CreateIndexes(bool useStandardIndex = true);
+
+        // sets the index caching mode for the readers
+        void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
+
+        //const int GetReferenceID(const string& refName) const;
+
+        // utility
+        void PrintFilenames(void);
+        void DumpAlignmentIndex(void);
+        void UpdateAlignments(void); // updates our alignment cache
+
+    // private implementation
+    private:
+
+        // the set of readers and alignments which we operate on, maintained throughout the life of this class
+        std::vector<std::pair<BamReader*, BamAlignment*> > readers;
+
+        // readers and alignments sorted by reference id and position, to keep track of the lowest (next) alignment
+        // when a reader reaches EOF, its entry is removed from this index
+        AlignmentIndex alignments;
+
+        std::vector<std::string> fileNames;
+};
+
+} // namespace BamTools
+
+#endif // BAMMULTIREADER_H