Examples with Resource org.broadinstitute.hellbender.utils.io.Resource used on opensource projects

Example 16 with Resource

use of org.broadinstitute.hellbender.utils.io.Resource in project gatk by broadinstitute.

the class PlotACNVResults method writeSegmentedAlleleFractionPlot.

/**
     * @param sampleName Sample name derived from input files
     * @param contigNames List containing contig names
     * @param contigLengths List containing contig lengths (same order as contigNames)
     */
private void writeSegmentedAlleleFractionPlot(final String sampleName, final List<String> contigNames, final List<Integer> contigLengths) {
    //names separated by delimiter
    final String contigNamesArg = contigNames.stream().collect(Collectors.joining(CONTIG_DELIMITER));
    //lengths separated by delimiter
    final String contigLengthsArg = contigLengths.stream().map(Object::toString).collect(Collectors.joining(CONTIG_DELIMITER));
    final String outputDirArg = addTrailingSlashIfNecessary(outputDir);
    final RScriptExecutor executor = new RScriptExecutor();
    //this runs the R statement "source("CNVPlottingLibrary.R")" before the main script runs
    executor.addScript(new Resource(CNV_PLOTTING_R_LIBRARY, PlotSegmentedCopyRatio.class));
    executor.addScript(new Resource(ACNV_PLOTTING_R_SCRIPT, PlotACNVResults.class));
    //--args is needed for Rscript to recognize other arguments properly
    executor.addArgs("--args", "--sample_name=" + sampleName, "--snp_counts_file=" + snpCountsFile, "--tangent_file=" + tangentFile, "--segments_file=" + segmentsFile, "--contig_names=" + contigNamesArg, "--contig_lengths=" + contigLengthsArg, "--output_dir=" + outputDirArg, "--output_prefix=" + outputPrefix);
    executor.exec();
}