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Add minimum base quality thresholding to depth of coverage via getBaseAndMappingFilteredPileup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2371 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-12-15 22:58:30 +00:00
parent 2deae95df9
commit 1035abc85f
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -52,6 +52,9 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
@Argument(fullName="minMAPQ", shortName ="minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
protected int excludeMAPQBelowThis = -1;
@Argument(fullName = "minBaseQualityScore", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public Integer minBaseQ = -1;
@Argument(fullName="minDepth", shortName ="minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
protected int minDepthForPercentage = -1;
@ -112,7 +115,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
// fill in and print all of the per-locus coverage data, then return it to reduce
ReadBackedPileup pileup = context.getPileup();
ReadBackedPileup pileup = context.getPileup().getBaseAndMappingFilteredPileup(minBaseQ, -1);
DoCInfo info = new DoCInfo();
info.totalCoverage = pileup.size();