28 lines
981 B
Java
Executable File
28 lines
981 B
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.LocusContext;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Feb 22, 2009
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* Time: 2:52:28 PM
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* To change this template use File | Settings | File Templates.
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*/
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public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
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// Do we actually want to operate on the context?
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public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
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return true; // We are keeping all the reads
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}
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// Map over the org.broadinstitute.sting.gatk.LocusContext
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public abstract MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
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// Given result of map function
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public abstract ReduceType reduceInit();
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public abstract ReduceType reduce(MapType value, ReduceType sum);
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}
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