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Merge pull request #243 from broadinstitute/mc_turn_off_downsampling_in_diagnose_targets 

Turn off downsampling for DiagnoseTargets
This commit is contained in:
Mark DePristo 2013-05-29 09:48:08 -07:00
parent 3516daff52 f1affa9fbb
commit 677e6bd6cf
1 changed files with 2 additions and 0 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -52,6 +52,7 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -110,6 +111,7 @@ import java.util.*;
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@By(value = DataSource.READS) @By(value = DataSource.READS)
@PartitionBy(PartitionType.INTERVAL) @PartitionBy(PartitionType.INTERVAL)
@Downsample(by = DownsampleType.NONE)
public class DiagnoseTargets extends LocusWalker<Long, Long> { public class DiagnoseTargets extends LocusWalker<Long, Long> {
private static final String AVG_INTERVAL_DP_KEY = "IDP"; private static final String AVG_INTERVAL_DP_KEY = "IDP";