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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
This commit is contained in:
aaron 2010-04-02 20:55:19 +00:00
parent 5a3622b051
commit 8017fb123f
2 changed files with 2 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java → java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -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<Map<String,int[]>, CoverageAggregator> implements TreeReducible<CoverageAggregator> {
public class DepthOfCoverageWalker extends LocusWalker<Map<String,int[]>, CoverageAggregator> implements TreeReducible<CoverageAggregator> {
@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)

1
packages/GenomeAnalysisTK.xml
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@ -18,6 +18,7 @@
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Basic qc walkers -->
<class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
<class name="org.broadinstitute.sting.gatk.refdata.tracks.builders.RODTrackBuilder" />
<class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />