Modified handling of BamAlignmentSupportData. This fix should allow BamWriter::SaveA...

[bamtools.git] / BamReader.cpp

diff --git a/BamReader.cpp b/BamReader.cpp
index 578cccfc23f91ccb18fe698ad280d6c593da9490..fcd17b16151c9562f10bb25734b01dc7f288321b 100644 (file)
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 9 July 2010 (DB)\r
+// Last modified: 15 July 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
 // Institute.\r
@@ -350,8 +350,8 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
     bAlignment.TagData.resize(tagDataLength);\r
     memcpy((char*)bAlignment.TagData.data(), tagData, tagDataLength);\r
     \r
-    // set support data parsed flag\r
-    bAlignment.SupportData.IsParsed = true;\r
+    // clear the core-only flag\r
+    bAlignment.SupportData.HasCoreOnly = false;\r
     \r
     // return success\r
     return true;\r
@@ -423,6 +423,9 @@ bool BamReader::BamReaderPrivate::GetNextAlignmentCore(BamAlignment& bAlignment)
     // if valid alignment available\r
     if ( LoadNextAlignment(bAlignment) ) {\r
 \r
+        // set core-only flag\r
+        bAlignment.SupportData.HasCoreOnly = true;\r
+      \r
         // if region not specified, return success\r
         if ( !IsLeftBoundSpecified ) return true;\r
 \r