From 2309d19f6f2f20dfbb155f1b677ab3abe8309e00 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 1 Oct 2009 14:34:36 +0000
Subject: [PATCH] Bug fix from Michael Ross: mark second read in sequence as
 second of pair.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1753 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/playground/tools/FastqToBam.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
index 509ec887b..c8b1d443c 100755
--- a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
@@ -79,7 +79,7 @@ public class FastqToBam extends CommandLineProgram {
                 sr2.setReadPairedFlag(true);
                 sr2.setAttribute("RG", READ_GROUP_NAME);
                 sr2.setFirstOfPairFlag(false);
-                sr2.setSecondOfPairFlag(false);
+                sr2.setSecondOfPairFlag(true);
                 sr2.setMateUnmappedFlag(true);
             }