From c2f0db969b91b323c2fc991cc6319afb9c3f9fc6 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 29 Aug 2011 13:48:10 -0400
Subject: [PATCH] Don't use the default deletion value from UG if not asking to
 have it set

---
 .../gatk/walkers/validation/GenotypeAndValidateWalker.java   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index 00a506fab..b616a0ebe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -303,7 +303,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         uac.alleles = alleles;
         if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
         if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
-        if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
+        if (deletions >= 0)
+            uac.MAX_DELETION_FRACTION = deletions;
+        else
+            uac.MAX_DELETION_FRACTION = 1.0;
         if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
         if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;