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Added a stateless walker to give the average depth of coverage for given reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@233 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-03-31 02:33:59 +00:00
parent 89c1762aa9
commit 007ecc8616
1 changed files with 28 additions and 0 deletions
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28
java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java 100644
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package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import java.util.List;
@WalkerName("Average_Depth_Of_Coverage")
public class AvgDepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
return context.getReads().size();
}
public Pair<Long, Long> reduceInit() { return new Pair<Long, Long>((long)0,(long)0); }
public Pair<Long, Long> reduce(Integer value, Pair<Long, Long> sum) {
long left = new Long(value.longValue() + sum.getFirst().longValue());
long right = new Long(sum.getSecond().longValue() + 1);
return new Pair<Long, Long>(left, right);
}
public void onTraversalDone(Pair<Long, Long> result) {
System.out.println("Average depth of coverage is: " + ((double)result.getFirst() / (double)result.getSecond()));
}
}