From 1aa40833521378c5b6f2cc754443ad744c219733 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 Apr 2011 17:16:41 +0000
Subject: [PATCH] Fortunately this code isn't used by anyone right now, but it
 needs to be fixed before someone unwitingly does: flags were wrong according
 to the SAM spec.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5584 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 3757120f8..5f2f35154 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -192,8 +192,8 @@ public class ReadUtils {
         readFlagNames.put(0x8, "MateUnmapped");
         readFlagNames.put(0x10, "Forward");
         //readFlagNames.put(0x20, "MateForward");
-        readFlagNames.put(0x4, "FirstOfPair");
-        readFlagNames.put(0x8, "SecondOfPair");
+        readFlagNames.put(0x40, "FirstOfPair");
+        readFlagNames.put(0x80, "SecondOfPair");
         readFlagNames.put(0x100, "NotPrimary");
         readFlagNames.put(0x200, "NON-PF");
         readFlagNames.put(0x400, "Duplicate");