46 lines
1.6 KiB
Java
46 lines
1.6 KiB
Java
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package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.gatk.LocusContext;
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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 java.util.List;
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import java.util.Arrays;
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import java.util.ArrayList;
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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: hanna
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* Date: 13 Apr, 2009
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* Time: 11:23:14 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer> {
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public LocusContext map(RefMetaDataTracker tracker, char ref, LocusContext context) {
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out.printf( "In map: ref = %c, loc = %s, reads = %s%n", ref,
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context.getLocation(),
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Arrays.deepToString( getReadNames(context.getReads()) ) );
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return context;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(LocusContext context, Integer sum) {
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out.printf( "In reduce: loc = %s, reads = %s, sum =%d%n", context.getLocation(),
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Arrays.deepToString( getReadNames(context.getReads()) ),
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sum );
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return sum + 1;
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}
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private String[] getReadNames( List<SAMRecord> reads ) {
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String[] readNames = new String[ reads.size() ];
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for( int i = 0; i < reads.size(); i++ )
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readNames[i] = reads.get(i).getReadName();
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return readNames;
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}
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}
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