public static void testReaderWriter(
final VariantContextIOTest tester,
final VCFHeader header,
final List<VariantContext> expected,
final Iterable<VariantContext> vcs,
final boolean recurse)
throws IOException {
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);
writeVCsToFile(writer, header, vcs);
// ensure writing of expected == actual
final VariantContextContainer p = tester.readAllVCs(tmpFile);
final Iterable<VariantContext> actual = p.getVCs();
assertEquals(actual, expected);
if (recurse) {
// if we are doing a recursive test, grab a fresh iterator over the written values
final Iterable<VariantContext> read = tester.readAllVCs(tmpFile).getVCs();
testReaderWriter(tester, p.getHeader(), expected, read, false);
}
}
private static void makeEmpiricalTests() throws IOException {
if (ENABLE_SOURCE_VCF_TESTS) {
for (final File file : testSourceVCFs) {
VCFCodec codec = new VCFCodec();
VariantContextContainer x = readAllVCs(file, codec);
List<VariantContext> fullyDecoded = new ArrayList<VariantContext>();
for (final VariantContext raw : x.getVCs()) {
if (raw != null) fullyDecoded.add(raw.fullyDecode(x.getHeader(), false));
}
TEST_DATAs.add(new VariantContextTestData(x.getHeader(), fullyDecoded));
}
}
}
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());
}
}
}
}
}
public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile)
throws IOException {
final VariantContextContainer vcfData = readAllVCs(vcfFile, new VCFCodec());
final VariantContextContainer bcfData = readAllVCs(bcfFile, new BCF2Codec());
assertEquals(bcfData.getHeader(), vcfData.getHeader());
assertEquals(bcfData.getVCs(), vcfData.getVCs());
}
