diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 7bcb01612..a715516af 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -58,7 +58,7 @@ import java.util.*; public class IndelRealigner extends ReadWalker { public static final String ORIGINAL_CIGAR_TAG = "OC"; - public static final String ORIGINAL_START_TAG = "OS"; + public static final String ORIGINAL_POSITION_TAG = "OP"; public static final String PROGRAM_RECORD_NAME = "GATK IndelRealigner"; @Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true) @@ -1179,7 +1179,7 @@ public class IndelRealigner extends ReadWalker { if ( !NO_ORIGINAL_ALIGNMENT_TAGS ) { read.setAttribute(ORIGINAL_CIGAR_TAG, read.getCigar().toString()); if ( newStart != read.getAlignmentStart() ) - read.setAttribute(ORIGINAL_START_TAG, read.getAlignmentStart()); + read.setAttribute(ORIGINAL_POSITION_TAG, read.getAlignmentStart()); } // if it's a paired end read, we need to update the insert size diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index fe2798aee..b441ff453 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerLod5() { - String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "18fca887d1eb7dc300e717ae03b9da62"}; + String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "18fca887d1eb7dc300e717ae03b9da62"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, @@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerLod50() { - String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "9537e4f195ce5840136f60fb61201369"}; + String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "9537e4f195ce5840136f60fb61201369"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, @@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerKnownsOnly() { - String[] md5s = {"f50b9bddd78ed6fb820d2cbdfbff8300", "1091436c40d5ba557d85662999cc0c1d"}; + String[] md5s = {"7084d4e543bc756730ab306768028530", "1091436c40d5ba557d85662999cc0c1d"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly", 2,