X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamMultiReader.h;h=37ad7652d46d0c8a38f61dbd138c9724c7d1eb01;hb=f6288f9f90747418a5d3c61b7713bee8e3a16112;hp=f1a2bb242e450785c5cacf32517d393a93fc9e1a;hpb=aa89df8c4510f88b2101ce91e8c46b99387560bd;p=bamtools.git

diff --git a/BamMultiReader.h b/BamMultiReader.h
index f1a2bb2..37ad765 100644
--- a/BamMultiReader.h
+++ b/BamMultiReader.h
@@ -15,6 +15,7 @@
 #include <string>
 #include <map>
 #include <utility> // for pair
+#include <sstream>
 
 using namespace std;
 
@@ -27,6 +28,7 @@ namespace BamTools {
 // index mapping reference/position pairings to bamreaders and their alignments
 typedef multimap<pair<int, int>, pair<BamReader*, BamAlignment*> > AlignmentIndex;
 
+
 class BamMultiReader {
 
     // constructor / destructor
@@ -41,17 +43,31 @@ class BamMultiReader {
         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
+        void Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);
+
         // performs random-access jump to reference, position
         bool Jump(int refID, int position = 0);
-        // opens BAM files (and optional BAM index files, if provided)
-        //void Open(const vector<std::string&> filenames, const vector<std::string&> indexFilenames);
-        void Open(const vector<string> filenames, bool openIndexes = true);
+
+        // 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);
 
@@ -63,6 +79,10 @@ class BamMultiReader {
 
         // 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);
 
@@ -86,13 +106,14 @@ class BamMultiReader {
         // ----------------------
 
         // creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")
-        bool CreateIndexes(void);
+        bool CreateIndexes(bool useDefaultIndex = true);
 
         //const int GetReferenceID(const string& refName) const;
 
         // utility
         void PrintFilenames(void);
         void DumpAlignmentIndex(void);
+        void UpdateAlignments(void); // updates our alignment cache
 
     // private implementation
     private: