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Simple count intervals walker, as per my recent email to GSAMembers. Never use this. It doesn't behave the way you think it does. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3905 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-07-30 03:39:23 +00:00
parent 9132c98eec
commit 3e3f8c7692
1 changed files with 47 additions and 0 deletions
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java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java 100755
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package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.List;
/**
* Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
* very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
* This was its very first use.
*/
public class CountIntervals extends RefWalker<GenomeLoc, Pair<GenomeLoc,Long>> {
public Pair<GenomeLoc,Long> reduceInit() {
return new Pair<GenomeLoc,Long>(null,0l);
}
public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) {
return null;
}
return ref.getLocus();
}
public Pair<GenomeLoc,Long> reduce(GenomeLoc loc, Pair<GenomeLoc,Long> prev) {
if ( prev.first == null || prev.first.distance(loc) > 1 ) {
prev.second ++;
}
prev.first = loc;
return prev;
}
public void onTraversalDone(Pair<GenomeLoc,Long> finalReduce ) {
out.printf("Number of contiguous intervals: %d",finalReduce.second);
}
}