From 13c800417e5a8d7054315c70b09f2b1325a310d7 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 17 Apr 2012 15:51:23 -0400
Subject: [PATCH] Handle NPE in UG indel code: deletions immediately preceding
 insertions were not handled well in the code.

---
 .../sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index b9422b6e5..e64a4f42d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -146,6 +146,10 @@ public class ConsensusAlleleCounter {
                 String indelString = p.getEventBases();
 
                 if ( p.isBeforeInsertion() ) {
+                    // edge case: ignore a deletion immediately preceding an insertion as p.getEventBases() returns null [EB]
+                    if ( indelString == null )
+                        continue;
+
                     boolean foundKey = false;
                     // copy of hashmap into temp arrayList
                     ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>();