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();
}
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());
}
}
}
}
}
