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Minor modification: adding an argument to make slightly more general. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3907 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-30 05:20:20 +00:00
parent db54d63fc7
commit 9231d13252
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -18,6 +19,8 @@ import java.util.List;
* This was its very first use.
*/
public class CountIntervals extends RefWalker<Long, Long> {
@Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false)
int numOverlaps = 2;
public Long reduceInit() {
return 0l;
@ -45,7 +48,7 @@ public class CountIntervals extends RefWalker<Long, Long> {
public void onTraversalDone(List<Pair<GenomeLoc,Long>> finalReduce) {
long count = 0;
for ( Pair<GenomeLoc,Long> g : finalReduce ) {
if ( g.second > 1) {
if ( g.second >= numOverlaps) {
count ++;
}
}