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Implementation of the find and diagnose Queue script 

-- Added 'uncovered intervals' output for FindCoveredIntervals
-- updated scala script to make use of it.
This commit is contained in:
Mauricio Carneiro 2013-02-19 21:07:36 -05:00
parent 15a8f6d82e
commit e3f01673e1
1 changed files with 6 additions and 3 deletions
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9
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -70,6 +70,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Output(required = true)
private PrintStream out;
@Argument(fullName = "uncovered", shortName = "u", required = false, doc = "output intervals that fail the coverage threshold instead")
private boolean outputUncovered = false;
@Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false)
private int coverageThreshold = 20;
@ -86,10 +89,10 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Override
public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
if (activeRegion.isActive())
if ((!outputUncovered && activeRegion.isActive()) || (outputUncovered && !activeRegion.isActive()))
return activeRegion.getLocation();
else
return null;
return null;
}
@Override