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

Example 11 with Resource

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

the class QualityScoreDistribution method finish.

@Override
protected void finish() {
    // Built the Histograms out of the long[]s
    final Histogram<Byte> qHisto = new Histogram<>("QUALITY", "COUNT_OF_Q");
    final Histogram<Byte> oqHisto = new Histogram<>("QUALITY", "COUNT_OF_OQ");
    for (int i = 0; i < qCounts.length; ++i) {
        if (qCounts[i] > 0)
            qHisto.increment((byte) i, (double) qCounts[i]);
        if (oqCounts[i] > 0)
            oqHisto.increment((byte) i, (double) oqCounts[i]);
    }
    final MetricsFile<?, Byte> metrics = getMetricsFile();
    metrics.addHistogram(qHisto);
    if (!oqHisto.isEmpty())
        metrics.addHistogram(oqHisto);
    metrics.write(OUTPUT);
    if (qHisto.isEmpty() && oqHisto.isEmpty()) {
        log.warn("No valid bases found in input file. No plot will be produced.");
    } else if (PRODUCE_PLOT) {
        // Now run R to generate a chart
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, QualityScoreDistribution.class));
        executor.addArgs(OUTPUT.getAbsolutePath(), CHART_OUTPUT.getAbsolutePath(), INPUT.getName(), plotSubtitle);
        executor.exec();
    }
}

Example 12 with Resource

use of org.broadinstitute.hellbender.utils.io.Resource in project gatk-protected 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();
}

Example 13 with Resource

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

the class PlotSegmentedCopyRatio method writeSegmentedCopyRatioPlots.

/**
     * @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 writeSegmentedCopyRatioPlots(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));
    //names separated by delimiter
    final String contigLengthsArg = contigLengths.stream().map(Object::toString).collect(Collectors.joining(CONTIG_DELIMITER));
    final String outputDirArg = addTrailingSlashIfNecessary(outputDir);
    final String isLog2InputArg = isLog2Input ? "TRUE" : "FALSE";
    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(COPY_RATIO_PLOTTING_R_SCRIPT, PlotSegmentedCopyRatio.class));
    //--args is needed for Rscript to recognize other arguments properly
    executor.addArgs("--args", "--sample_name=" + sampleName, "--tangent_file=" + tangentFile, "--pre_tangent_file=" + preTangentFile, "--segments_file=" + segmentsFile, "--contig_names=" + contigNamesArg, "--contig_lengths=" + contigLengthsArg, "--output_dir=" + outputDirArg, "--output_prefix=" + outputPrefix, "--is_log2_input=" + isLog2InputArg);
    executor.exec();
}

Example 14 with Resource

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

the class CollectGcBiasMetrics method finish.

/////////////////////////////////////////////////////////////////////////////
// Synthesize the normalized coverage metrics and write it all out to a file
/////////////////////////////////////////////////////////////////////////////
@Override
protected void finish() {
    final MetricsFile<GcBiasDetailMetrics, ?> metricsFile = getMetricsFile();
    final double totalWindows = sum(windowsByGc);
    final double totalReads = sum(readsByGc);
    final double meanReadsPerWindow = totalReads / totalWindows;
    final double minimumWindowsToCountInSummary = totalWindows * this.MINIMUM_GENOME_FRACTION;
    for (int i = 0; i < windowsByGc.length; ++i) {
        if (windowsByGc[i] == 0)
            continue;
        final GcBiasDetailMetrics m = new GcBiasDetailMetrics();
        m.GC = i;
        m.WINDOWS = windowsByGc[i];
        m.READ_STARTS = readsByGc[i];
        if (errorsByGc[i] > 0)
            m.MEAN_BASE_QUALITY = QualityUtil.getPhredScoreFromObsAndErrors(basesByGc[i], errorsByGc[i]);
        m.NORMALIZED_COVERAGE = (m.READ_STARTS / (double) m.WINDOWS) / meanReadsPerWindow;
        m.ERROR_BAR_WIDTH = (Math.sqrt(m.READ_STARTS) / (double) m.WINDOWS) / meanReadsPerWindow;
        metricsFile.addMetric(m);
    }
    metricsFile.write(OUTPUT);
    // Synthesize the high level metrics
    if (SUMMARY_OUTPUT != null) {
        final MetricsFile<GcBiasSummaryMetrics, ?> summaryMetricsFile = getMetricsFile();
        final GcBiasSummaryMetrics summary = new GcBiasSummaryMetrics();
        summary.WINDOW_SIZE = this.WINDOW_SIZE;
        summary.TOTAL_CLUSTERS = this.totalClusters;
        summary.ALIGNED_READS = this.totalAlignedReads;
        calculateDropoutMetrics(metricsFile.getMetrics(), summary);
        summaryMetricsFile.addMetric(summary);
        summaryMetricsFile.write(SUMMARY_OUTPUT);
    }
    // Plot the results
    final NumberFormat fmt = NumberFormat.getIntegerInstance();
    fmt.setGroupingUsed(true);
    final String subtitle = "Total clusters: " + fmt.format(this.totalClusters) + ", Aligned reads: " + fmt.format(this.totalAlignedReads);
    String title = INPUT.getName().replace(".duplicates_marked", "").replace(".aligned.bam", "");
    title += "." + saveHeader;
    if (PRODUCE_PLOT) {
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, CollectGcBiasMetrics.class));
        executor.addArgs(OUTPUT.getAbsolutePath(), CHART_OUTPUT.getAbsolutePath(), title, subtitle, String.valueOf(WINDOW_SIZE));
        executor.exec();
    }
}

Example 15 with Resource

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

the class CollectBaseDistributionByCycle method finish.

@Override
protected void finish() {
    final MetricsFile<BaseDistributionByCycleMetrics, ?> metrics = getMetricsFile();
    hist.addToMetricsFile(metrics);
    metrics.write(OUTPUT);
    if (hist.isEmpty()) {
        log.warn("No valid bases found in input file. No plot will be produced.");
    } else if (PRODUCE_PLOT) {
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, CollectBaseDistributionByCycle.class));
        executor.addArgs(OUTPUT.getAbsolutePath(), CHART_OUTPUT.getAbsolutePath(), INPUT.getName(), plotSubtitle);
        executor.exec();
    }
}