Cleaned up index file handling throughout toolkit. Did this by adding a FileExists...

[bamtools.git] / src / api / BamMultiReader.h

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index bd36d7160e0d18aee8d63c8699262c4a296695bc..dce7042f8d1248c14661bc8a1a6c73ae166448ea 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 20 July 2010 (DB)\r
+// Last modified: 2 September 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Functionality for simultaneously reading multiple BAM files\r
 // ***************************************************************************\r
@@ -59,8 +59,15 @@ class BamMultiReader {
         // indexes.\r
         // @coreMode - setup our first alignments using GetNextAlignmentCore();\r
         // also useful for merging\r
+        // @useDefaultIndex - look for default BAM index ".bai" first.  If false, \r
+        // or if ".bai" does not exist, will look for BamTools index ".bti".  If \r
+        // neither exist, will open without an index\r
         bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);\r
 \r
+        // returns whether underlying BAM readers ALL have an index loaded\r
+        // this is useful to indicate whether Jump() or SetRegion() are possible\r
+        bool IsIndexLoaded(void) const;\r
+        \r
         // performs random-access jump to reference, position\r
         bool Jump(int refID, int position = 0);\r
 \r