From b8cd959461ab7e55c07139f9dcaebc0851406ffd Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Thu, 22 Mar 2012 10:06:22 -0400
Subject: [PATCH] Potential corner condition bug fix: protect against null
 pointer exceptions when computing consensus indel bases when UG is
 discovering alt alleles. If an alt allele has non-standard bases, skip allele
 gracefully instead of adding null object into list

---
 .../genotyper/IndelGenotypeLikelihoodsCalculationModel.java     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1b73ef1d7..21f11d2ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -240,6 +240,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                     refAllele = Allele.create(refBases, true);
                     altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
                 }
+                else continue; // don't go on with this allele if refBases are non-standard
             } else {
                 // insertion case
                 if (Allele.acceptableAlleleBases(s)) {
@@ -247,6 +248,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                     altAllele = Allele.create(s, false);
                     stop = loc.getStart();
                 }
+                else continue; // go on to next allele if consensus insertion has any non-standard base.
             }