From 8017fb123f43a6846fd095ed8743f5d83c0dc22b Mon Sep 17 00:00:00 2001 From: aaron Date: Fri, 2 Apr 2010 20:55:19 +0000 Subject: [PATCH] changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a --- .../{DepthOfCoverage.java => DepthOfCoverageWalker.java} | 2 +- packages/GenomeAnalysisTK.xml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) rename java/src/org/broadinstitute/sting/gatk/walkers/coverage/{DepthOfCoverage.java => DepthOfCoverageWalker.java} (99%) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java rename to java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 42d897c91..ce41bdaf0 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -49,7 +49,7 @@ import java.util.*; // todo -- allow for user to set linear binning (default is logarithmic) // todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now @By(DataSource.REFERENCE) -public class DepthOfCoverage extends LocusWalker, CoverageAggregator> implements TreeReducible { +public class DepthOfCoverageWalker extends LocusWalker, CoverageAggregator> implements TreeReducible { @Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false) int start = 1; @Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false) diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml index 6484e9100..eb12892b3 100644 --- a/packages/GenomeAnalysisTK.xml +++ b/packages/GenomeAnalysisTK.xml @@ -18,6 +18,7 @@ +