From a17bf145f619922ff3516bb9397263d1a6662e3f Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 29 Jun 2009 19:05:33 +0000
Subject: [PATCH] fix to respond to the change in IndelLikelihood constructor.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1119 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/SingleSampleGenotyper.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index 9d43067e6..a9771cce0 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -229,7 +229,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
      */
     private IndelLikelihood callIndel(LocusContext context, List<SAMRecord> reads, List<Integer> offsets) {
         String[] indels = BasicPileup.indelPileup(reads, offsets);
-        IndelLikelihood indelCall = new IndelLikelihood(indels);
+        IndelLikelihood indelCall = new IndelLikelihood(indels, 1e-4);
 
         if (! indelCall.getType().equals("ref")) {
             System.out.printf("INDEL %s %s\n", context.getLocation(), indelCall);