From 20c1fbaf0f7b71a1ee16e463e0f464bfdd8c0158 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Tue, 6 Mar 2012 14:22:45 -0500 Subject: [PATCH] Fixing a merge (turning off downsampling on DoC) --- .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 94f9eb6c5..833dce932 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -29,6 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -115,6 +116,7 @@ import java.util.*; // 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) @PartitionBy(PartitionType.NONE) +@Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE) public class DepthOfCoverageWalker extends LocusWalker>, CoveragePartitioner> implements TreeReducible { @Output @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})