Examples with StringHeader htsjdk.samtools.metrics.StringHeader used on opensource projects

Example 1 with StringHeader

use of htsjdk.samtools.metrics.StringHeader in project gatk by broadinstitute.

the class CommandLineProgram method instanceMainPostParseArgs.

public Object instanceMainPostParseArgs() {
    // Provide one temp directory if the caller didn't
    if (this.TMP_DIR == null)
        this.TMP_DIR = new ArrayList<>();
    if (this.TMP_DIR.isEmpty())
        TMP_DIR.add(IOUtil.getDefaultTmpDir());
    // Build the default headers
    final ZonedDateTime startDateTime = ZonedDateTime.now();
    this.defaultHeaders.add(new StringHeader(commandLine));
    this.defaultHeaders.add(new StringHeader("Started on: " + Utils.getDateTimeForDisplay(startDateTime)));
    // propagate the VERBOSITY level to logging frameworks
    LoggingUtils.setLoggingLevel(VERBOSITY);
    for (final File f : TMP_DIR) {
        // need a tmp_dir. If this fails, the problem will be discovered downstream.
        if (!f.exists())
            f.mkdirs();
        f.setReadable(true, false);
        f.setWritable(true, false);
        // in loop so that last one takes effect
        System.setProperty("java.io.tmpdir", f.getAbsolutePath());
    }
    //Set defaults (note: setting them here means they are not controllable by the user)
    if (!useJdkDeflater) {
        BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory());
    }
    if (!useJdkInflater) {
        BlockGunzipper.setDefaultInflaterFactory(new IntelInflaterFactory());
    }
    if (!QUIET) {
        System.err.println("[" + Utils.getDateTimeForDisplay(startDateTime) + "] " + commandLine);
        // Output a one liner about who/where and what software/os we're running on
        try {
            System.err.println("[" + Utils.getDateTimeForDisplay(startDateTime) + "] Executing as " + System.getProperty("user.name") + "@" + InetAddress.getLocalHost().getHostName() + " on " + System.getProperty("os.name") + " " + System.getProperty("os.version") + " " + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") + " " + System.getProperty("java.runtime.version") + "; Version: " + getVersion());
            // Print important settings to the logger:
            printSettings();
        } catch (final Exception e) {
        /* Unpossible! */
        }
    }
    try {
        return runTool();
    } finally {
        // Emit the time even if program throws
        if (!QUIET) {
            final ZonedDateTime endDateTime = ZonedDateTime.now();
            final double elapsedMinutes = (Duration.between(startDateTime, endDateTime).toMillis()) / (1000d * 60d);
            final String elapsedString = new DecimalFormat("#,##0.00").format(elapsedMinutes);
            System.err.println("[" + Utils.getDateTimeForDisplay(endDateTime) + "] " + getClass().getName() + " done. Elapsed time: " + elapsedString + " minutes.");
            System.err.println("Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
        }
    }
}