29 lines
1.0 KiB
Java
Executable File
29 lines
1.0 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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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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@Requires({DataSource.READS, DataSource.REFERENCE_BASES})
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public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
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public boolean requiresOrderedReads() { return false; }
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// Do we actually want to operate on the context?
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/** Must return true for reads that need to be processed. Reads, for which this method return false will
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* be skipped by the engine and never passed to the walker.
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*/
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public boolean filter(char[] ref, 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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// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
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public abstract MapType map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker);
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}
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