Merge branch 'master' of git://github.com/pezmaster31/bamtools

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

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index dce7042f8d1248c14661bc8a1a6c73ae166448ea..cc30326b59f0773750739dda999df6e89bb153f0 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: 2 September 2010 (DB)\r
+// Last modified: 3 September 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Functionality for simultaneously reading multiple BAM files\r
 // ***************************************************************************\r
@@ -59,10 +59,9 @@ 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
+        // @preferStandardIndex - look for standard BAM index ".bai" first.  If false, \r
+        // will look for BamTools index ".bti".  \r
+        bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = 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