From 01265f78e66b1f30069b5afe999e07e8d8cc3753 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 1 Aug 2012 10:50:00 -0400
Subject: [PATCH] Add sanity check and possible bug fix for forum user: if
 haplotypes cannot be created from given alleles when genotyping indels (e.g.
 too close to contig boundary, etc.) in pool mode, empty allele list,
 signifying site can't be genotyped

---
 .../PoolIndelGenotypeLikelihoodsCalculationModel.java         | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
index c2bac4455..c87ed04a0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
@@ -105,6 +105,10 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi
             haplotypeMap.clear();
         }
         IndelGenotypeLikelihoodsCalculationModel.getHaplotypeMapFromAlleles(alleles, ref, ref.getLocus(), haplotypeMap);
+
+        // sanity check: if haplotype map couldn't be created, clear allele list
+        if (haplotypeMap.isEmpty())
+            alleles.clear();
         return alleles;
 
     }