Examples of org.broadinstitute.gatk.utils.R.RScriptExecutor

org.broadinstitute.gatk.utils.R.RScriptExecutor
Generic service for executing RScripts

        if(VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) {
            // Print out an info message to make it clear why the tranches plot is not generated
            logger.info("Tranches plot will not be generated since we are running in INDEL mode");
        } else {
            // Execute the RScript command to plot the table of truth values
            RScriptExecutor executor = new RScriptExecutor();
            executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class));
            executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV);
            // Print out the command line to make it clear to the user what is being executed and how one might modify it
            logger.info("Executing: " + executor.getApproximateCommandLine());
            executor.exec();
        }
    }

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        stream.println("}");


        stream.close();


        // Execute Rscript command to generate the clustering plots
        RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(RSCRIPT_FILE);
        logger.info("Executing: " + executor.getApproximateCommandLine());
        executor.exec();
     }

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     * @param csvFile location of the intermediary file
     * @param exampleReportFile where the report arguments are collected from.
     * @param output result plot file name.
     */
    public static void generatePlots(final File csvFile, final File exampleReportFile, final File output) {
        final RScriptExecutor executor = new RScriptExecutor();
        executor.setExceptOnError(true);
        executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class));
        executor.addArgs(csvFile.getAbsolutePath());
        executor.addArgs(exampleReportFile.getAbsolutePath());
        executor.addArgs(output.getAbsolutePath());
        Logger.getLogger(RecalUtils.class).debug("R command line: " + executor.getApproximateCommandLine());
        executor.exec();
    }

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        executor.exec();
    }


    private static void outputRecalibrationPlot(final File csvFile, final RecalibrationArgumentCollection RAC) {


        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class));
        executor.addArgs(csvFile.getAbsolutePath());
        executor.addArgs(RAC.RECAL_TABLE_FILE.getAbsolutePath());
        executor.exec();
    }

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Related Classes of org.broadinstitute.gatk.utils.R.RScriptExecutor

org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator

org.broadinstitute.gatk.utils.recalibration.RecalUtils

org.broadinstitute.gatk.utils.runtime.ProcessController

org.broadinstitute.gatk.utils.runtime.ProcessSettings

java.io.File

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