38 lines
1.4 KiB
Java
Executable File
38 lines
1.4 KiB
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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.List;
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import net.sf.samtools.SAMRecord;
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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 DuplicateWalker<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(GenomeLoc loc, byte[] refBases, LocusContext context, List<SAMRecord> duplicateReads) {
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return true; // We are keeping all the reads
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}
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/**
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* These two functions state whether we're don't make any sense without reads (requiresRead())
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* or whether we can't take any reads at all (cannotHandleRead())
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*/
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public boolean requiresReads() { return true; }
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public boolean cannotHandleReads() { return false; }
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// Map over the org.broadinstitute.sting.gatk.LocusContext
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public abstract MapType map(GenomeLoc loc, byte[] refBases, LocusContext context, List<SAMRecord> duplicateReads);
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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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} |