From 317fac8dff7f27363810c61b665125e0a383b883 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 3 Mar 2010 01:03:10 +0000
Subject: [PATCH] Better error message for --assume_single_sample_reads screw
 up

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2916 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java      | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 165a89e84..d72e2201c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -205,7 +205,11 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
 
         // use multi-sample mode if we have multiple samples or the output type allows it
         else {
-            writer.addMultiSampleCall(value.genotypes, value.variation);
+            try {
+                writer.addMultiSampleCall(value.genotypes, value.variation);
+            } catch (IllegalArgumentException e) {
+                throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");    
+            }
         }
 
         return sum;