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Updating random walkers to new rod system

This commit is contained in:
Eric Banks 2011-08-15 13:29:31 -04:00
parent 3d56bbf087
commit fc2c21433b
1 changed files with 7 additions and 2 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
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@ -2,16 +2,18 @@ package org.broadinstitute.sting.gatk.walkers.qc;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
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.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.Collections;
import java.util.List; import java.util.List;
/** /**
@ -23,6 +25,9 @@ public class CountIntervals extends RefWalker<Long, Long> {
@Output @Output
PrintStream out; PrintStream out;
@Input(fullName="check", shortName = "check", doc="Any number of RODs", required=false)
public List<RodBinding<Feature>> features = Collections.emptyList();
@Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false) @Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false)
int numOverlaps = 2; int numOverlaps = 2;
@ -37,7 +42,7 @@ public class CountIntervals extends RefWalker<Long, Long> {
return null; return null;
} }
List<Feature> checkIntervals = tracker.getValues(Feature.class, "check"); List<Feature> checkIntervals = tracker.getValues(features);
return (long) checkIntervals.size(); return (long) checkIntervals.size();
} }