integration of SetRegion into BamMultiReader

[bamtools.git] / BamMultiReader.h

diff --git a/BamMultiReader.h b/BamMultiReader.h
index 3d9024c40ce9927e13e3588acb82d4d09b7711a7..e5960df03f13c84a70e392962b45e8a69afed590 100644 (file)
--- a/BamMultiReader.h
+++ b/BamMultiReader.h
@@ -43,6 +43,9 @@ class BamMultiReader {
         int CurrentRefID;\r
         int CurrentLeft;\r
 \r
+        // region under analysis, specified using SetRegion\r
+        BamRegion Region;\r
+\r
         // ----------------------\r
         // BAM file operations\r
         // ----------------------\r
@@ -61,6 +64,10 @@ class BamMultiReader {
         // performs random-access jump to reference, position\r
         bool Jump(int refID, int position = 0);\r
 \r
+        // sets the target region\r
+        bool SetRegion(const BamRegion& region);\r
+        bool SetRegion(const int&, const int&, const int&, const int&); // convenience function to above\r
+\r
         // returns file pointers to beginning of alignments\r
         bool Rewind(void);\r
 \r
@@ -106,6 +113,7 @@ class BamMultiReader {
         // utility\r
         void PrintFilenames(void);\r
         void DumpAlignmentIndex(void);\r
+        void UpdateAlignments(void); // updates our alignment cache\r
 \r
     // private implementation\r
     private:\r