Moved BamAlignment data structure out to its own .h/.cpp. BamAux.h was getting over...

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

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 6e863b6beded3fbded2b9d70b0442b4c1276dbaf..132c95b826dbe854750c883fe38d20a4a2ab4806 100644 (file)
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 3 September 2010 (DB)\r
+// Last modified: 18 September 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
 // Institute.\r
@@ -14,11 +14,8 @@
 #ifndef BAMREADER_H\r
 #define BAMREADER_H\r
 \r
-// C++ includes\r
 #include <string>\r
-\r
-// BamTools includes\r
-#include "BamAux.h"\r
+#include "BamAlignment.h"\r
 \r
 namespace BamTools {\r
   \r
@@ -42,7 +39,7 @@ class BamReader {
         bool IsIndexLoaded(void) const;\r
         // returns whether reader is open for reading or not\r
         bool IsOpen(void) const;\r
-        // performs random-access jump to reference, position\r
+        // performs random-access jump using (reference, position) as a left-bound\r
         bool Jump(int refID, int position = 0);\r
         // opens BAM file (and optional BAM index file, if provided)\r
         // @lookForIndex - if no indexFilename provided, look for an existing index file\r
@@ -67,9 +64,8 @@ class BamReader {
         bool GetNextAlignment(BamAlignment& bAlignment);\r
         \r
         // retrieves next available alignment core data (returns success/fail)\r
-        // ** DOES NOT parse any character data (read name, 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
+        // ** DOES NOT parse any character data (read name, bases, qualities, tag data) **\r
+        // useful for operations requiring ONLY aligner-related information (refId/position, alignment flags, CIGAR, mapQuality, etc)\r
         bool GetNextAlignmentCore(BamAlignment& bAlignment);\r
 \r
         // ----------------------\r