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Add an option to filter the read bases that are taking into account for the coveraged intervals. For that, new two arguments were added: minBaseQuality and minMappingQuality

This commit is contained in:
Ami Levy-Moonshine 2013-11-07 17:16:14 -05:00
parent 6ad841cec5
commit e6ef37de1d
1 changed files with 14 additions and 1 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
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@ -101,11 +101,24 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false)
private int coverageThreshold = 20;
@Argument(fullName = "minBaseQuality", shortName = "minBQ", doc = "The minimum allowable base quality score to be counted for coverage",required = false)
private int minBaseQuality = 0;
@Argument(fullName = "minMappingQuality", shortName = "minMQ", doc = "The minimum allowable mapping quality score to be counted for coverage",required = false)
private int minMappingQuality = 0;
@Override
// Look to see if the region has sufficient coverage
public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
int depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
int depth;
if(minBaseQuality == 0 && minMappingQuality == 0)
depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
else
depth = context.getBasePileup().getBaseAndMappingFilteredPileup(minBaseQuality,minMappingQuality).depthOfCoverage();
// note the linear probability scale
return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1));