42 lines
1.4 KiB
Java
42 lines
1.4 KiB
Java
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package org.broadinstitute.sting.gatk.walkers;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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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 BasicReadWalker<MapType, ReduceType> implements ReadWalker<MapType, ReduceType> {
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public String getName() {
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// Return name of class, trimming 'Walker' from the end if present.
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// TODO: Duplicate of BasicLociWalker.getName(). Eliminate duplication.
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String className = getClass().getSimpleName();
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if(className.endsWith(Walker.class.getSimpleName()))
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return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
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else
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return className;
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}
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public void initialize() { }
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public boolean requiresOrderedReads() { return false; }
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public boolean filter(LocusContext context, SAMRecord read) {
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// We are keeping all the reads
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return true;
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}
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public void onTraversalDone() {
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;
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}
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// Three basic abstract function that *must* be overridden
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public abstract MapType map(LocusContext context, SAMRecord read);
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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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