From 2a4a4b0aab85efb15d642a1a539bd089108ce3fd Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Aug 2010 23:17:16 +0000
Subject: [PATCH] VariantRecalibrator now calls plot_Tranches directly so it
 works on the farm

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3993 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/VariantRecalibrator.java        | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

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 a82878f6f..7410a8299 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -250,12 +250,15 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
         // Execute Rscript command to plot the optimization curve
         // Print out the command line to make it clear to the user what is being executed and how one might modify it
-        final String rScriptCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_OptimizationCurve.R" + " " + OUTPUT_PREFIX + ".dat" + " " + TARGET_TITV;
-        logger.info( rScriptCommandLine );
+        final String rScriptOptimizationCurveCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_OptimizationCurve.R" + " " + OUTPUT_PREFIX + ".dat" + " " + TARGET_TITV;
+        final String rScriptTranchesCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Tranches.R" + " " + OUTPUT_PREFIX + ".dat" + " " + TARGET_TITV;
+        logger.info( rScriptOptimizationCurveCommandLine );
+        logger.info( rScriptTranchesCommandLine );
 
         // Execute the RScript command to plot the table of truth values
         try {
-            Runtime.getRuntime().exec( rScriptCommandLine );
+            Runtime.getRuntime().exec( rScriptOptimizationCurveCommandLine );
+            Runtime.getRuntime().exec( rScriptTranchesCommandLine );
         } 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.");
         }