From bffd3cca6fe26fe31a6fa5a33745dcaee0139c56 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 20 Sep 2011 15:07:06 -0400
Subject: [PATCH] Bug fix for reduced read; only adds regular bases for
 calculation

-- No longer passes on deletions for genotyping
---
 .../walkers/genotyper/DiploidSNPGenotypeLikelihoods.java   | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index 5f6865d04..ec180f0cd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -276,8 +276,11 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
         if ( elt.isReducedRead() ) {
             // reduced read representation
             byte qual = elt.getReducedQual();
-            add(obsBase, qual, (byte)0, (byte)0, elt.getReducedCount()); // fast calculation of n identical likelihoods
-            return elt.getReducedCount(); // we added nObs bases here
+            if ( BaseUtils.isRegularBase( elt.getBase() )) {
+                add(obsBase, qual, (byte)0, (byte)0, elt.getReducedCount()); // fast calculation of n identical likelihoods
+                return elt.getReducedCount(); // we added nObs bases here
+            } else // odd bases or deletions => don't use them
+                return 0;
         } else {
             byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
             return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0;