From 6efbcd99f13186d916d29c385a86ed5c685a6609 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 17 Jul 2012 14:38:36 -0400 Subject: [PATCH] HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling. --- .../sting/gatk/walkers/annotator/BaseQualityRankSumTest.java | 3 ++- .../sting/gatk/walkers/annotator/ClippingRankSumTest.java | 2 +- .../gatk/walkers/annotator/MappingQualityRankSumTest.java | 3 ++- .../sting/gatk/walkers/annotator/RankSumTest.java | 2 +- .../sting/gatk/walkers/annotator/ReadPosRankSumTest.java | 3 ++- 5 files changed, 8 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 8bc5f06f4..0b919da18 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; @@ -15,7 +16,7 @@ import java.util.*; * The u-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele). * Note that the base quality rank sum test can not be calculated for homozygous sites. */ -public class BaseQualityRankSumTest extends RankSumTest { +public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation { public List getKeyNames() { return Arrays.asList("BaseQRankSum"); } public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java index 5403e19dc..f41a40621 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java @@ -18,7 +18,7 @@ import java.util.*; * Date: 6/28/12 */ -public class ClippingRankSumTest /*extends RankSumTest*/ { +public class ClippingRankSumTest extends RankSumTest { public List getKeyNames() { return Arrays.asList("ClippingRankSum"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 4ce19e824..c7fb7ecba 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -16,7 +17,7 @@ import java.util.*; * The u-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele) * Note that the mapping quality rank sum test can not be calculated for homozygous sites. */ -public class MappingQualityRankSumTest extends RankSumTest { +public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation { public List getKeyNames() { return Arrays.asList("MQRankSum"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index cdef1f77c..bf66958e0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -28,7 +28,7 @@ import java.util.Map; /** * Abstract root for all RankSum based annotations */ -public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { +public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation { static final double INDEL_LIKELIHOOD_THRESH = 0.1; static final boolean DEBUG = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 40bf6bbd8..630344992 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -4,6 +4,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -21,7 +22,7 @@ import java.util.*; * The u-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error). * Note that the read position rank sum test can not be calculated for homozygous sites. */ -public class ReadPosRankSumTest extends RankSumTest { +public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation { public List getKeyNames() { return Arrays.asList("ReadPosRankSum");