X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamReader.cpp;h=fcd17b16151c9562f10bb25734b01dc7f288321b;hb=a2400c1ecfd075271b14c2c83aae0dc42bf7e42a;hp=578cccfc23f91ccb18fe698ad280d6c593da9490;hpb=f68dccd9031c84f73b9754c1fbced63bd8551f6f;p=bamtools.git

diff --git a/BamReader.cpp b/BamReader.cpp
index 578cccf..fcd17b1 100644
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 9 July 2010 (DB)
+// Last modified: 15 July 2010 (DB)
 // ---------------------------------------------------------------------------
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -350,8 +350,8 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
     bAlignment.TagData.resize(tagDataLength);
     memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);
     
-    // set support data parsed flag
-    bAlignment.SupportData.IsParsed = true;
+    // clear the core-only flag
+    bAlignment.SupportData.HasCoreOnly = false;
     
     // return success
     return true;
@@ -423,6 +423,9 @@ bool BamReader::BamReaderPrivate::GetNextAlignmentCore(BamAlignment& bAlignment)
     // if valid alignment available
     if ( LoadNextAlignment(bAlignment) ) {
 
+        // set core-only flag
+        bAlignment.SupportData.HasCoreOnly = true;
+      
         // if region not specified, return success
         if ( !IsLeftBoundSpecified ) return true;