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Updating FindCoveredIntervals to use the changes to the ActiveRegionWalker.

This commit is contained in:
Ryan Poplin 2012-07-30 12:16:27 -04:00
parent 13591b169f
commit 7ed06ee7b9
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream; import java.io.PrintStream;
@ -47,13 +48,13 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Override @Override
// Look to see if the region has sufficient coverage // 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()); int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup());
// note the linear probability scale // note the linear probability scale
int coverageThreshold = 20; int coverageThreshold = 20;
return Math.min((double) depth / coverageThreshold, 1); return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1));
} }