From 275575462f9bf708d223c9ba497e5908a6deced9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 26 Dec 2012 15:46:21 -0500
Subject: [PATCH] Protect against non-standard ref bases.  Ryan, please review.

---
 .../walkers/haplotypecaller/LikelihoodCalculationEngine.java | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 59f241cdb..e1a1ed6d2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -120,6 +120,11 @@ public class LikelihoodCalculationEngine {
 
             for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
                 final Haplotype haplotype = haplotypes.get(jjj);
+
+                // TODO -- need to test against a reference/position with non-standard bases
+                if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
+                    continue;
+
                 final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
                 previousHaplotypeSeen = haplotype;