From 505f588768b5140a36d8ea47d9fb8d7848e08e25 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 20 May 2009 15:38:51 +0000
Subject: [PATCH] Forgot to say that the mate is unmapped too.  This is
 necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/AnnotateSecondaryBase.java               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
index 0fef3b827..d2a8a216d 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
@@ -180,6 +180,7 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
         SAMRecord sr = new SAMRecord(sfh);
 
         sr.setReadName(runBarcode + ":" + rr.getReadKey() + "#0");
+        sr.setMateUnmappedFlag(true);
         sr.setReadUmappedFlag(true);
         sr.setReadString(rr.getSequenceAsString());
         sr.setBaseQualities(rr.getQuals());