Example #1
0
  protected int doWork() {
    IoUtil.assertFileIsReadable(INPUT);
    IoUtil.assertFileIsWritable(OUTPUT);

    final SAMFileReader in = new SAMFileReader(INPUT);

    // create the read group we'll be using
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
    rg.setLibrary(RGLB);
    rg.setPlatform(RGPL);
    rg.setSample(RGSM);
    rg.setPlatformUnit(RGPU);
    if (RGCN != null) rg.setSequencingCenter(RGCN);
    if (RGDS != null) rg.setDescription(RGDS);
    if (RGDT != null) rg.setRunDate(RGDT);

    log.info(
        String.format(
            "Created read group ID=%s PL=%s LB=%s SM=%s%n",
            rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));

    // create the new header and output file
    final SAMFileHeader inHeader = in.getFileHeader();
    final SAMFileHeader outHeader = inHeader.clone();
    outHeader.setReadGroups(Arrays.asList(rg));
    if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);

    final SAMFileWriter outWriter =
        new SAMFileWriterFactory()
            .makeSAMOrBAMWriter(
                outHeader, outHeader.getSortOrder() == inHeader.getSortOrder(), OUTPUT);

    final ProgressLogger progress = new ProgressLogger(log);
    for (final SAMRecord read : in) {
      read.setAttribute(SAMTag.RG.name(), RGID);
      outWriter.addAlignment(read);
      progress.record(read);
    }

    // cleanup
    in.close();
    outWriter.close();
    return 0;
  }
Example #2
0
  /**
   * Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance
   * to do the real work.
   */
  protected int doWork() {
    IoUtil.assertFileIsReadable(getProbeIntervals());
    IoUtil.assertFileIsReadable(TARGET_INTERVALS);
    IoUtil.assertFileIsReadable(INPUT);
    IoUtil.assertFileIsWritable(OUTPUT);
    if (PER_TARGET_COVERAGE != null) IoUtil.assertFileIsWritable(PER_TARGET_COVERAGE);

    final SAMFileReader samReader = new SAMFileReader(INPUT);

    final File probeIntervals = getProbeIntervals();

    // Validate that the targets and baits have the same references as the reads file
    SequenceUtil.assertSequenceDictionariesEqual(
        samReader.getFileHeader().getSequenceDictionary(),
        IntervalList.fromFile(TARGET_INTERVALS).getHeader().getSequenceDictionary(),
        INPUT,
        TARGET_INTERVALS);
    SequenceUtil.assertSequenceDictionariesEqual(
        samReader.getFileHeader().getSequenceDictionary(),
        IntervalList.fromFile(probeIntervals).getHeader().getSequenceDictionary(),
        INPUT,
        probeIntervals);

    ReferenceSequenceFile ref = null;
    if (REFERENCE_SEQUENCE != null) {
      IoUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
      ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
      SequenceUtil.assertSequenceDictionariesEqual(
          samReader.getFileHeader().getSequenceDictionary(),
          ref.getSequenceDictionary(),
          INPUT,
          REFERENCE_SEQUENCE);
    }

    final TargetMetricsCollector collector =
        makeCollector(
            METRIC_ACCUMULATION_LEVEL,
            samReader.getFileHeader().getReadGroups(),
            ref,
            PER_TARGET_COVERAGE,
            TARGET_INTERVALS,
            probeIntervals,
            getProbeSetName());

    // Add each record to the requested collectors
    final Iterator<SAMRecord> records = samReader.iterator();
    final ProgressLogger progress = new ProgressLogger(log);

    while (records.hasNext()) {
      final SAMRecord sam = records.next();
      collector.acceptRecord(sam, null);
      progress.record(sam);
    }

    // Write the output file
    final MetricsFile<HsMetrics, Integer> metrics = getMetricsFile();
    collector.finish();

    collector.addAllLevelsToFile(metrics);

    metrics.write(OUTPUT);

    return 0;
  }