fixed potential bug with previous commit

[bamtools.git] / BamReader.h

diff --git a/BamReader.h b/BamReader.h
index 6332cde74bf76ecd539f9f073d8244483dc6ec1c..88cc74a25d3cfd04ab90e7957dbfe808b313121e 100644 (file)
--- a/BamReader.h
+++ b/BamReader.h
@@ -1,9 +1,9 @@
 // ***************************************************************************\r
-// BamReader.h (c) 2009 Derek Barnett, Michael Strömberg\r
+// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 8 December 2009 (DB)\r
+// Last modified: 8 June 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
 // Institute.\r
@@ -51,6 +51,11 @@ class BamReader {
 \r
         // retrieves next available alignment (returns success/fail)\r
         bool GetNextAlignment(BamAlignment& bAlignment);\r
+        // retrieves next available alignment core data (returns success/fail)\r
+        // ** DOES NOT parse any character data (bases, qualities, tag data)\r
+        //    these can be accessed, if necessary, from the supportData \r
+        // useful for operations requiring ONLY positional or other alignment-related information\r
+        bool GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);\r
 \r
         // ----------------------\r
         // access auxiliary data\r
@@ -59,11 +64,13 @@ class BamReader {
         // returns SAM header text\r
         const std::string GetHeaderText(void) const;\r
         // returns number of reference sequences\r
-        const int GetReferenceCount(void) const;\r
+        int GetReferenceCount(void) const;\r
         // returns vector of reference objects\r
         const BamTools::RefVector GetReferenceData(void) const;\r
         // returns reference id (used for BamReader::Jump()) for the given reference name\r
-        const int GetReferenceID(const std::string& refName) const;\r
+        int GetReferenceID(const std::string& refName) const;\r
+        // returns the name of the file associated with this BamReader\r
+        const std::string GetFilename(void) const;\r
 \r
         // ----------------------\r
         // BAM index operations\r