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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
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depristo 2010-08-09 23:17:16 +00:00
parent c2c0c1f57c
commit 2a4a4b0aab
1 changed files with 6 additions and 3 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -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.");
}