From b004489c6deb90d2ec0618915a8c8a903d82d0e5 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 1 Nov 2011 17:11:47 -0400
Subject: [PATCH] Moving ReduceRead TAG to GATKSAMRecord

ReduceReads are now a feature of a GATKSAMRecord, so the tag and the special methods needed to use it will now be housed by the GATKSAMRecord.
---
 .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java  | 3 ++-
 .../java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 2 --
 .../test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index d6c0b68b8..ede75817a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -43,6 +43,7 @@ import java.util.Map;
  *
  */
 public class GATKSAMRecord extends BAMRecord {
+    public static final String REDUCED_READ_QUALITY_TAG = "RR";
     // the SAMRecord data we're caching
     private String mReadString = null;
     private GATKSAMReadGroupRecord mReadGroup = null;
@@ -151,7 +152,7 @@ public class GATKSAMRecord extends BAMRecord {
 
     public byte[] getReducedReadCounts() {
         if ( ! retrievedReduceReadCounts ) {
-            reducedReadCounts = getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
+            reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG);
             retrievedReduceReadCounts = true;
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index f8e4927ed..3504f59dc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -51,8 +51,6 @@ public class ReadUtils {
     //
     // ----------------------------------------------------------------------------------------------------
 
-    public static final String REDUCED_READ_QUALITY_TAG = "RQ";
-
     // ----------------------------------------------------------------------------------------------------
     //
     // General utilities
diff --git a/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
index 59a6ecb8d..ed50a6f92 100755
--- a/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
@@ -29,7 +29,7 @@ public class ReadUtilsUnitTest extends BaseTest {
         reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
         reducedRead.setReadBases(BASES.getBytes());
         reducedRead.setBaseQualityString(QUALS);
-        reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
+        reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
     }
 
     private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {