Examples of org.broadinstitute.gatk.utils.io.Resource

Package org.broadinstitute.gatk.utils.io

Examples of org.broadinstitute.gatk.utils.io.Resource

org.broadinstitute.gatk.utils.io.Resource
Stores a resource by path and a relative class.

            // 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();
        }

View Full Code Here

     * @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();

View Full Code Here

    }


    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();
    }

View Full Code Here

     * @return a non-null GATK
     */
    @Requires("name != null")
    @Ensures("result != null")
    private static String getAWSKey(final String name) {
        final Resource resource = new Resource(name, GATKRunReport.class);
        return decryptAWSKey(resource.getResourceContentsAsStream());
    }

View Full Code Here

TOP

Related Classes of org.broadinstitute.gatk.utils.io.Resource

org.broadinstitute.gatk.engine.phonehome.GATKRunReport

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

org.broadinstitute.gatk.utils.recalibration.RecalUtils

java.io.InputStream

java.io.File

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.