From 3a8d9237850ee623de83043140e23d42b4bcd6a5 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 4 Aug 2009 20:12:16 +0000 Subject: [PATCH] minor output changes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/variants/VECAlleleBalance.java | 3 ++- .../gatk/walkers/variants/VariantFiltrationWalker.java | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java index 65ba0ce19..d79ed723a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Pair; +import org.broadinstitute.sting.utils.GenotypeUtils; public class VECAlleleBalance implements VariantExclusionCriterion { //extends RatioFilter { //final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed; @@ -62,7 +63,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends Pair counts = scoreVariant(ref, pileup, variant); int n = counts.first + counts.second; ratio = counts.first.doubleValue() / (double)n; - exclude = (1.0 - ratio) < lowThreshold || ratio > highThreshold; + exclude = GenotypeUtils.isHet(variant) && ((1.0 - ratio) < lowThreshold || ratio > highThreshold); } public boolean useZeroQualityReads() { return false; } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java index 182f27381..48e50ea74 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java @@ -62,7 +62,7 @@ public class VariantFiltrationWalker extends LocusWalker { if (LEARNING) { PrintWriter studyWriter = new PrintWriter(VARIANTS_OUT_HEAD + "." + STUDY_NAME); swriters.put(STUDY_NAME, studyWriter); - studyWriter.print("#Chr\tPosition\t"); + studyWriter.print("Chr\tPosition\t"); } requestedFeatures = new ArrayList(); @@ -257,7 +257,7 @@ public class VariantFiltrationWalker extends LocusWalker { if (LEARNING) { rodDbSNP dbsnp = (rodDbSNP)tracker.lookup(knownSNPDBName, null); if ( dbsnp == null ) - swriters.get(STUDY_NAME).print("no\tno\t"); + swriters.get(STUDY_NAME).print("false\tfalse\t"); else swriters.get(STUDY_NAME).print(dbsnp.isSNP() + "\t" + dbsnp.isHapmap() + "\t"); swriters.get(STUDY_NAME).println(GenotypeUtils.isHet(variant));