From 463f80c03ed05a4b1c69aac6e26cea0c28b6461f Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 31 Aug 2009 03:37:24 +0000 Subject: [PATCH] Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1487 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/gatk/walkers/variants/IVFNull.java | 2 ++ .../sting/playground/gatk/walkers/variants/RatioFilter.java | 2 +- .../playground/gatk/walkers/variants/VECAlleleBalance.java | 2 +- .../gatk/walkers/variants/VariantFiltrationWalker.java | 2 +- 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java index 586ec6258..d51ae9e94 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java @@ -17,4 +17,6 @@ public class IVFNull implements IndependentVariantFeature { public String getStudyInfo() { return ""; } + + public boolean useZeroQualityReads() { return false; } } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java index 3ffb30773..b0f7d66d1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java @@ -261,7 +261,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion { rodVariants variant = context.getVariant(); char ref = context.getReferenceContext().getBase(); - ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext()); + ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads())); if ( applyToVariant(variant) ) { Pair counts = scoreVariant(ref, pileup, variant); GenotypeFeatureData gfd = dataTable.get(orderedBases(variant.getBestGenotype())); 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 72d4030d4..95c43dfac 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 @@ -57,7 +57,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends char ref = context.getReferenceContext().getBase(); rodVariants variant = context.getVariant(); - ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext()); + ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads())); Pair counts = scoreVariant(ref, pileup, variant); int n = counts.first + counts.second; ratio = counts.first.doubleValue() / (double)n; 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 3d3b9b9a6..d14d7b800 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 @@ -210,7 +210,7 @@ public class VariantFiltrationWalker extends LocusWalker { if (VERBOSE) { out.println("Original:\n" + variant); } - GenomeLoc loc = context.getAlignmentContext().getLocation(); + GenomeLoc loc = context.getAlignmentContext(true).getLocation(); paramsWriter.print(loc.getContig() + "\t" + loc.getStart() + "\t"); // Apply features that modify the likelihoods and LOD scores