コード例 #1
0
    public String toString() {
      StringBuilder b = new StringBuilder();
      b.append("VariantContextTestData: [");
      final VariantContext vc = vcs.get(0);
      final VariantContextBuilder builder = new VariantContextBuilder(vc);
      builder.noGenotypes();
      b.append(builder.make().toString());
      if (vc.getNSamples() < 5) {
        for (final Genotype g : vc.getGenotypes()) b.append(g.toString());
      } else {
        b.append(" nGenotypes = ").append(vc.getNSamples());
      }

      if (vcs.size() > 1)
        b.append(" ----- with another ").append(vcs.size() - 1).append(" VariantContext records");
      b.append("]");
      return b.toString();
    }
コード例 #2
0
  public static void testReaderWriterWithMissingGenotypes(
      final VariantContextIOTest tester, final VariantContextTestData data) throws IOException {
    final int nSamples = data.header.getNGenotypeSamples();
    if (nSamples > 2) {
      for (final VariantContext vc : data.vcs)
        if (vc.isSymbolic())
          // cannot handle symbolic alleles because they may be weird non-call VCFs
          return;

      final File tmpFile = File.createTempFile("testReaderWriter", tester.getExtension());
      tmpFile.deleteOnExit();

      // write expected to disk
      final EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
      final VariantContextWriter writer = tester.makeWriter(tmpFile, options);

      final Set<String> samplesInVCF = new HashSet<String>(data.header.getGenotypeSamples());
      final List<String> missingSamples = Arrays.asList("MISSING1", "MISSING2");
      final List<String> allSamples = new ArrayList<String>(missingSamples);
      allSamples.addAll(samplesInVCF);

      final VCFHeader header = new VCFHeader(data.header.getMetaDataInInputOrder(), allSamples);
      writeVCsToFile(writer, header, data.vcs);

      // ensure writing of expected == actual
      final VariantContextContainer p = tester.readAllVCs(tmpFile);
      final Iterable<VariantContext> actual = p.getVCs();

      int i = 0;
      for (final VariantContext readVC : actual) {
        if (readVC == null) continue; // sometimes we read null records...
        final VariantContext expected = data.vcs.get(i++);
        for (final Genotype g : readVC.getGenotypes()) {
          Assert.assertTrue(allSamples.contains(g.getSampleName()));
          if (samplesInVCF.contains(g.getSampleName())) {
            assertEquals(g, expected.getGenotype(g.getSampleName()));
          } else {
            // missing
            Assert.assertTrue(g.isNoCall());
          }
        }
      }
    }
  }