From df4e001a070c95b0eccbefe800fffd9da4a86925 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 3 Dec 2009 17:34:49 +0000 Subject: [PATCH] Renamed to more accurately describe its function. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a --- ...verageEvalWalker.java => SnpCallRateByCoverageWalker.java} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{CoverageEvalWalker.java => SnpCallRateByCoverageWalker.java} (98%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java index f9166b9f8..1a0258d4d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java @@ -26,7 +26,7 @@ import java.util.List; * Time: 12:38:17 PM * To change this template use File | Settings | File Templates. */ -public class CoverageEvalWalker extends LocusWalker, String> { +public class SnpCallRateByCoverageWalker extends LocusWalker, String> { // Control what goes into the variants file and what format that file should have @Argument(fullName="lod_threshold", shortName="lod", doc="The lod threshold on which variants should be filtered", required=false) public Double LOD_THRESHOLD = 5.0; @@ -47,7 +47,7 @@ public class CoverageEvalWalker extends LocusWalker, String> { } public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - return (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 && context.getReads().size() != 0); + return (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 && context.getPileup().size() != 0); } public List map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {