From bf60ed0b259cf1e5eda2376e11c011ce05e6012c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 Aug 2010 13:11:27 +0000
Subject: [PATCH] Needed it here too: warn user instead of dying if the R
 script cannot be executed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3929 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/GenerateVariantClustersWalker.java     | 2 +-
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 01fbe897c..21c5f7853 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -244,7 +244,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
             try {
                 Runtime.getRuntime().exec( rScriptCommandLine );
             } catch ( IOException e ) {
-                Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the recalibration proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
+                Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the clustering proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
             }
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index cf8460111..6ecdb0320 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -243,7 +243,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         try {
             Runtime.getRuntime().exec( rScriptCommandLine );
         } catch ( IOException e ) {
-            throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine );
+            Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the recalibration proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
         }
     }
 }