From d00b2c6599b2d20b4b926a0aa6c5649e3fbae20a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 9 Nov 2011 20:09:12 -0500 Subject: [PATCH] Adding a synthetic read for filtered data * Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data. * Synthetic reads can now have deletions (but not insertions) * New reduced read tag for filtered data synthetic reads *(RF)* * Sliding window header now keeps information of consensus and filtered data * Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads --- .../org/broadinstitute/sting/utils/sam/GATKSAMRecord.java | 6 ++++-- .../org/broadinstitute/sting/utils/ReadUtilsUnitTest.java | 2 +- 2 files changed, 5 insertions(+), 3 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 9e07b1112..d95570d9b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -46,7 +46,9 @@ import java.util.Map; * */ public class GATKSAMRecord extends BAMRecord { - public static final String REDUCED_READ_QUALITY_TAG = "RR"; + public static final String REDUCED_READ_CONSENSUS_TAG = "RR"; + public static final String REDUCED_READ_FILTERED_TAG = "RF"; + // the SAMRecord data we're caching private String mReadString = null; private GATKSAMReadGroupRecord mReadGroup = null; @@ -173,7 +175,7 @@ public class GATKSAMRecord extends BAMRecord { public byte[] getReducedReadCounts() { if ( ! retrievedReduceReadCounts ) { - reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG); + reducedReadCounts = getByteArrayAttribute(REDUCED_READ_CONSENSUS_TAG); retrievedReduceReadCounts = true; } diff --git a/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java index bc39d714e..46134cd24 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(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS); + reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS); } private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) {