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) {