From 396bce1f28ee622f3ebfd1237e975a3cd30e16ba Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 9 Jan 2013 10:51:30 -0500
Subject: [PATCH] Reverting this change until we can figure out the right thing
 to do here.

---
 .../walkers/haplotypecaller/LikelihoodCalculationEngine.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 8e90285d9..e416b489b 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
@@ -124,8 +124,8 @@ public class LikelihoodCalculationEngine {
                 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;
+                //if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
+                //    continue;
 
                 final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
                 previousHaplotypeSeen = haplotype;