Java Code Examples for htsjdk.samtools.util.StringUtil#asEmptyIfNull()

The following examples show how to use htsjdk.samtools.util.StringUtil#asEmptyIfNull() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: MeanQualityByCycleSpark.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
private void saveResults(final MetricsFile<?, Integer> metrics, final SAMFileHeader readsHeader, final String inputFileName){
    MetricsUtils.saveMetrics(metrics, out);

    if (metrics.getAllHistograms().isEmpty()) {
        logger.warn("No valid bases found in input file.");
    } else if (chartOutput != null){
        // Now run R to generate a chart

        // If we're working with a single library, assign that library's name
        // as a suffix to the plot title
        final List<SAMReadGroupRecord> readGroups = readsHeader.getReadGroups();

        /*
         * A subtitle for the plot, usually corresponding to a library.
         */
        String plotSubtitle = "";
        if (readGroups.size() == 1) {
            plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
        }
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(getMeanQualityByCycleRScriptResource());
        executor.addArgs(out, chartOutput.getAbsolutePath(), inputFileName, plotSubtitle);
        executor.exec();
    }
}
Example 2
Source File: CollectBaseDistributionByCycleSpark.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
protected void saveResults(final MetricsFile<?, Integer> metrics, final SAMFileHeader readsHeader, final String inputFileName) {
    MetricsUtils.saveMetrics(metrics, out);

    if (metrics.getAllHistograms().isEmpty()) {
        logger.warn("No valid bases found in input file.");
    } else if (chartOutput != null) {
        // Now run R to generate a chart

        // If we're working with a single library, assign that library's name
        // as a suffix to the plot title
        final List<SAMReadGroupRecord> readGroups = readsHeader.getReadGroups();

        /*
         * A subtitle for the plot, usually corresponding to a library.
         */
        String plotSubtitle = "";
        if (readGroups.size() == 1) {
            plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
        }
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(getBaseDistributionByCycleRScriptResource());
        executor.addArgs(out, chartOutput.getAbsolutePath(), inputFileName, plotSubtitle);
        executor.exec();
    }
}
Example 3
Source File: CollectBaseDistributionByCycle.java    From picard with MIT License 5 votes vote down vote up 
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
    IOUtil.assertFileIsWritable(CHART_OUTPUT);
    final List<SAMReadGroupRecord> readGroups = header.getReadGroups();
    if (readGroups.size() == 1) {
        plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
    }
    hist = new HistogramGenerator();
}
Example 4
Source File: CollectWgsMetricsWithNonZeroCoverage.java    From picard with MIT License 5 votes vote down vote up 
@Override
protected int doWork() {
    IOUtil.assertFileIsWritable(CHART_OUTPUT);
    IOUtil.assertFileIsReadable(INPUT);

    // Initialize the SamReader, so the header is available prior to super.doWork, for getIntervalsToExamine call. */
    getSamReader();

    this.collector = new WgsMetricsWithNonZeroCoverageCollector(this, COVERAGE_CAP, getIntervalsToExamine());
    super.doWork();

    final List<SAMReadGroupRecord> readGroups = getSamFileHeader().getReadGroups();
    final String plotSubtitle = (readGroups.size() == 1) ? StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary()) : "";

    if (collector.areHistogramsEmpty()) {
        log.warn("No valid bases found in input file. No plot will be produced.");
    } else {
        final int rResult = RExecutor.executeFromClasspath("picard/analysis/wgsHistogram.R",
                OUTPUT.getAbsolutePath(),
                CHART_OUTPUT.getAbsolutePath(),
                INPUT.getName(),
                plotSubtitle);
        if (rResult != 0) {
            throw new PicardException("R script wgsHistogram.R failed with return code " + rResult);
        }
    }

    return 0;
}
Example 5
Source File: MeanQualityByCycle.java    From picard with MIT License 5 votes vote down vote up 
@Override
protected void setup(final SAMFileHeader header, final File samFile) {
    IOUtil.assertFileIsWritable(CHART_OUTPUT);
    // If we're working with a single library, assign that library's name
    // as a suffix to the plot title
    final List<SAMReadGroupRecord> readGroups = header.getReadGroups();
    if (readGroups.size() == 1) {
        plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
    }
}