From 7c8b17b45620a31d51f0733d2981c6821ddb1767 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Sep 2009 20:39:34 +0000
Subject: [PATCH] fix for SSG with pl name

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1591 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
index 8eaf4e72a..2b681a440 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
@@ -43,7 +43,7 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
     }
 
     public static SequencerPlatform standardizeSequencerPlatform( final String sequencerString ) {
-        String lcSequencerString = sequencerString.toLowerCase();
+        String lcSequencerString = sequencerString == null ? null : sequencerString.toLowerCase();
         if ( sequencerString != null && PLFieldToSequencerPlatform.containsKey(lcSequencerString) ) {
             return PLFieldToSequencerPlatform.get(lcSequencerString);
         } else {
@@ -259,6 +259,7 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
                 throw new RuntimeException("Unknown Sequencer platform for read " + read.format());
             else {
                 pl = defaultPlatform;
+                //System.out.printf("Using default platform %s", pl);
             }
         }