From 1035abc85f33a9b47c00e3fe507d9aeb577f1c96 Mon Sep 17 00:00:00 2001
From: andrewk <andrewk@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Dec 2009 22:58:30 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index b3a74168b..fa7195e26 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -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();