Method mainExec

src/main/java/com/rtg/vcf/VcfSplitCli.java:99–154

(OutputStream out, LogStream log)

  }

  @Override
  protected int mainExec(OutputStream out, LogStream log) throws IOException {
    final boolean gzip = !mFlags.isSet(CommonFlags.NO_GZIP);
    final boolean keepRef = mFlags.isSet(KEEP_REF);
    final boolean asyncOutput = (Boolean) mFlags.getValue(ASYNC);
    final VcfSubset.VcfSampleStripperFactory sampleStripperFact = new VcfSubset.VcfSampleStripperFactory(mFlags);
    try (final VcfReader reader = new VcfReaderFactory(mFlags).parser(new VcfSubsetParser(sampleStripperFact)).make(mFlags)) {
      final int numberSamples = reader.getHeader().getNumberOfSamples();
      if (numberSamples == 0) {
        throw new NoTalkbackSlimException("No samples to be output.");
      }
      final VcfWriter[] writers = new VcfWriter[numberSamples];
      final ArrayList<String> samples = new ArrayList<>(reader.getHeader().getSampleNames());
      try {
        final VcfWriterFactory f = new VcfWriterFactory(mFlags).addRunInfo(true).async(asyncOutput);
        for (int i = 0; i < numberSamples; ++i) {
          final String sample = samples.get(i);
          final File of = new File(outputDirectory(), sample);
          final File vcfFile = VcfUtils.getZippedVcfFileName(gzip, of);
          Diagnostic.userLog("Outputting sample '" + sample + "' to: " + vcfFile);
          final VcfHeader header = reader.getHeader().copy();
          header.removeAllSamples();
          header.addSampleName(sample);
          writers[i] = f.make(header, vcfFile);
        }
        while (reader.hasNext()) {
          final VcfRecord rec = reader.next();
          if (rec.hasFormat(VcfUtils.FORMAT_GENOTYPE)) {
            final List<String> gts = rec.getFormat(VcfUtils.FORMAT_GENOTYPE);
            final VcfRecord template = new VcfRecord(rec); // Work on a copy
            for (int i = 0; i < numberSamples; ++i) {
              final String gt = gts.get(i);
              final int[] gtArr = VcfUtils.splitGt(gt);
              if (VcfUtils.isValidGt(rec, gtArr) && VcfUtils.isNonMissingGt(gt)
                && (keepRef || hasAlt(gtArr))) {
                template.removeSamples();
                template.setNumberOfSamples(1);
                // Copy sample field values from original
                for (Map.Entry<String, ArrayList<String>> e : rec.getFormatAndSample().entrySet()) {
                  template.setFormatAndSample(e.getKey(), e.getValue().get(i), 0);
                }
                writers[i].write(asyncOutput ? new VcfRecord(template) : template);
              }
            }
          }
        }
      } finally {
        for (VcfWriter w : writers) {
          if (w != null) {
            w.close();
          }
        }
      }
    }
    return 0;
  }

  private boolean hasAlt(int[] gt) {