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Fixing a merge (turning off downsampling on DoC)

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Christopher Hartl 2012-03-06 14:22:45 -05:00
parent 129b5e7f6b
commit 20c1fbaf0f
1 changed files with 2 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -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<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
@Output
@Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})