70 lines
2.2 KiB
Java
70 lines
2.2 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.rodDbSNP;
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import net.sf.samtools.SAMRecord;
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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: 3:22:14 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class PileupWalker extends BasicLociWalker<Integer, Integer> {
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public void initialize() {
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}
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public String walkerType() { return "ByLocus"; }
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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 Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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String bases = "";
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String quals = "";
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for ( int i = 0; i < reads.size(); i++ ) {
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SAMRecord read = reads.get(i);
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int offset = offsets.get(i);
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bases += read.getReadString().charAt(offset);
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quals += read.getBaseQualityString().charAt(offset);
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}
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String rodString = "";
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for ( ReferenceOrderedDatum datum : rodData ) {
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if ( datum != null ) {
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if ( datum instanceof rodDbSNP) {
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rodDbSNP dbsnp = (rodDbSNP)datum;
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rodString += dbsnp.toMediumString();
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}
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else {
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rodString += datum.toSimpleString();
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}
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}
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}
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if ( rodString != "" )
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rodString = "[ROD: " + rodString + "]";
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if ( context.getLocation().getStart() % 1 == 0 ) {
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System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString);
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}
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return 1;
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}
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// Given result of map function
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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}
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