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Hahaha yes, ownage. This now works. 

BTW, Eric, thanks for forwarding the DepthOfCoverage thread to gsamembers. I'd forgotten about reduce by interval. Mighty helpful in this case!




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3906 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-30 04:23:02 +00:00
parent 3e3f8c7692
commit db54d63fc7
1 changed files with 21 additions and 14 deletions
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35
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java
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@ -17,31 +17,38 @@ import java.util.List;
* very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to. * 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. * This was its very first use.
*/ */
public class CountIntervals extends RefWalker<GenomeLoc, Pair<GenomeLoc,Long>> { public class CountIntervals extends RefWalker<Long, Long> {
public Pair<GenomeLoc,Long> reduceInit() { public Long reduceInit() {
return new Pair<GenomeLoc,Long>(null,0l); return 0l;
} }
public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public boolean isReduceByInterval() { return true; }
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) { if ( tracker == null ) {
return null; return null;
} }
return ref.getLocus(); List<GATKFeature> checkIntervals = tracker.getGATKFeatureMetaData("check",false);
return (long) checkIntervals.size();
} }
public Pair<GenomeLoc,Long> reduce(GenomeLoc loc, Pair<GenomeLoc,Long> prev) { public Long reduce(Long loc, Long prev) {
if ( prev.first == null || prev.first.distance(loc) > 1 ) { if ( loc == null ) {
prev.second ++; return 0l;
} else {
return Math.max(prev,loc);
} }
prev.first = loc;
return prev;
} }
public void onTraversalDone(Pair<GenomeLoc,Long> finalReduce ) { public void onTraversalDone(List<Pair<GenomeLoc,Long>> finalReduce) {
out.printf("Number of contiguous intervals: %d",finalReduce.second); long count = 0;
for ( Pair<GenomeLoc,Long> g : finalReduce ) {
if ( g.second > 1) {
count ++;
}
}
out.printf("Number of contiguous intervals: %d",count);
} }
} }