Method mainExec

src/main/java/com/rtg/vcf/VcfMerge.java:175–251

(final OutputStream out, final PrintStream err)

  }

  @Override
  protected int mainExec(final OutputStream out, final PrintStream err) throws IOException {
    final File outFile = (File) mFlags.getValue(OUTPUT_FLAG);
    final List<File> inputs = CommonFlags.getFileList(mFlags, CommonFlags.INPUT_LIST_FLAG, null, false);
    final HashSet<File> dupTest = new HashSet<>();
    for (final File f : inputs) {
      if (!dupTest.add(f.getCanonicalFile())) {
        throw new NoTalkbackSlimException("File: " + f.getPath() + " is specified more than once.");
      }
    }
    final Collection<String> extraHeaderLines = getHeaderLines(mFlags);
    final HashSet<String> forceMerge;
    if (mFlags.isSet(FORCE_MERGE_ALL)) {
      forceMerge = null;
    } else {
      final List<?> forceMergeRaw = mFlags.getValues(FORCE_MERGE);
      forceMerge = new HashSet<>();
      for (final Object o : forceMergeRaw) {
        forceMerge.add((String) o);
      }
    }
    final boolean gzip = !mFlags.isSet(NO_GZIP);
    final VariantStatistics stats = mFlags.isSet(STATS_FLAG) ? new VariantStatistics(null) : null;
    final ReferenceRanges<String> regions = CommonFlags.parseRegionOrBedRegions(mFlags);
    final VcfPositionZipper posZip = new VcfPositionZipper(regions, forceMerge, inputs.toArray(new File[0]));
    final VcfHeader header = posZip.getHeader();
    VcfUtils.addHeaderLines(header, extraHeaderLines);

    String defaultFormat = FORMAT_GENOTYPE;
    if (header.getFormatField(FORMAT_GENOTYPE) == null && header.getFormatLines().size() > 0) {
      defaultFormat = header.getFormatLines().get(0).getId();
    }

    final boolean stdout = FileUtils.isStdio(outFile);
    final File vcfFile = VcfUtils.getZippedVcfFileName(gzip, outFile);
    final VcfRecordMerger merger;
    if (mFlags.isSet(GT_MAJORITY)) {
      if (!FORMAT_GENOTYPE.equals(defaultFormat)) {
        throw new NoTalkbackSlimException("VCF header does not contain GT declaration");
      }
      merger = new VcfGtMajorityMerger();
    } else if (mFlags.isSet(NO_ALT_MERGE)) {
      merger = new VcfSameAltsMerger();
    } else {
      merger = new VcfRecordMerger();
    }
    merger.setHeader(header);
    merger.setDefaultFormat(defaultFormat);
    merger.setAllowMerging(!mFlags.isSet(NO_RECORD_MERGE));
    merger.setPaddingAware(!mFlags.isSet(NON_PADDING_AWARE));
    merger.setDropUnmergeable(!mFlags.isSet(PRESERVE_FORMATS));

    try (final VcfWriter w = new VcfWriterFactory(mFlags).addRunInfo(true).make(header, vcfFile)) {
      final ZipperCallback callback = (records, headers) -> {
        assert records.length > 0;
        final VcfRecord[] mergedArr = merger.mergeRecords(records, headers);
        for (VcfRecord merged : mergedArr) {
          if (stats != null) {