diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index c964b0b4b..0c856c6df 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; @@ -47,13 +48,13 @@ public class FindCoveredIntervals extends ActiveRegionWalker { @Override // Look to see if the region has sufficient coverage - public double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup()); // note the linear probability scale int coverageThreshold = 20; - return Math.min((double) depth / coverageThreshold, 1); + return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1)); }