From b694ca96331ad4fbde5edc0c457353483f1735ae Mon Sep 17 00:00:00 2001 From: delangel Date: Thu, 17 Jun 2010 17:45:48 +0000 Subject: [PATCH] Cleanup: Don't require likelihood ROD in Beagle parameters when generating output VCF. Likelihoods file is only an input to Beagle but the Walker that generates a VCF doesn't need it, so it's silly to ask for it and it's error-prone. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3579 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/BeagleOutputToVCFWalker.java | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java index cf5a8f61d..a583cd7c9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java @@ -55,7 +55,6 @@ import static java.lang.Math.log10; * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations. */ @Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME,type= VCFRecord.class)) -//@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="r2",type= ReferenceOrderedDatum.class), @RMD(name="beagleR2",type= BeagleR2ROD.class)}) public class BeagleOutputToVCFWalker extends RodWalker { @@ -67,13 +66,6 @@ public class BeagleOutputToVCFWalker extends RodWalker { public static final String INPUT_ROD_NAME = "inputvcf"; -/* - protected static BeagleFileReader gprobsReader = null; - - protected static BeagleFileReader phasedReader = null; - protected static BeagleFileReader likeReader = null; - protected static BeagleFileReader r2Reader = null; - */ protected static String line = null; // protected HashMap beagleSampleRecords; @@ -125,13 +117,6 @@ public class BeagleOutputToVCFWalker extends RodWalker { return 0; - List likerods = tracker.getReferenceMetaData("beagleLike"); - // ignore places where we don't have a variant - if ( likerods.size() == 0 ) - return 0; - - BeagleFeature beagleLikeFeature = (BeagleFeature)likerods.get(0); - List r2rods = tracker.getReferenceMetaData("beagleR2"); // ignore places where we don't have a variant