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BaseCoverageDistributions should be 'by reference' 

otherwise we miss all the 0 coverage spots.
This commit is contained in:
Mauricio Carneiro 2013-01-29 22:36:31 -05:00
parent e02dac03aa
commit 3d9a83c759
1 changed files with 3 additions and 0 deletions
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3
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
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@ -51,6 +51,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import java.io.PrintStream;
@ -62,6 +64,7 @@ import java.util.Map;
* Date: 1/27/13
* Time: 11:16 AM
*/
@By(DataSource.REFERENCE)
public class BaseCoverageDistribution extends LocusWalker<Integer, Map<Integer, Long>> {
@Output(required = true)
private PrintStream out;