From 9464dfdbf2a7d26c4e04ab7993c698bc440a3c7b Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 24 Sep 2012 14:06:07 -0400
Subject: [PATCH] Don't penalize the reduced reads for spanning deletions (when
 surrounding base quals are Q2s)

---
 .../sting/gatk/walkers/qc/AssessReducedCoverage.java            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
index fd407d105..d38c11594 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
@@ -99,7 +99,7 @@ public class AssessReducedCoverage extends LocusWalker<GenomeLoc, GenomeLoc> imp
         final Set<String> tags = new HashSet<String>(10);
 
         for ( final PileupElement p : pileup ) {
-            if ( (int)p.getQual() > 2 && p.getMappingQual() > 0 )
+            if ( (int)p.getQual() > 2 && p.getMappingQual() > 0 && !p.isDeletion() )
                 tags.addAll(getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags());
         }