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Moved avg depth of coverage functionality into the core depth of coverage 

walker.  Used new command line args for walkers.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-03-31 05:02:33 +00:00
parent 007ecc8616
commit 3896cc8f17
2 changed files with 18 additions and 35 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
View File

@ -2,7 +2,8 @@ package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Pair;
import java.util.List;
/**
@ -12,15 +13,25 @@ import java.util.List;
* Time: 3:22:14 PM
* To change this template use File | Settings | File Templates.
*/
public class DepthOfCoverageWalker extends LocusWalker<Integer, Integer> {
public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
@Argument(fullName="printall",required=false,defaultValue="true")
public String printAllLoci; // booleans don't work
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
return 1;
if (printAllLoci.equals("true"))
out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
return context.getReads().size();
}
public Integer reduceInit() { return 0; }
public Pair<Long, Long> reduceInit() { return new Pair<Long, Long>((long)0,(long)0); }
public Integer reduce(Integer value, Integer sum) {
return value + sum;
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) {
out.println("Average depth of coverage is: " + ((double)result.getFirst() / (double)result.getSecond()));
}
}

28
java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java
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@ -1,28 +0,0 @@
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()));
}
}