/**
* Assert that two variant contexts are actually equal
*
* @param actual
* @param expected
*/
public static void assertEquals(final VariantContext actual, final VariantContext expected) {
Assert.assertNotNull(actual, "VariantContext expected not null");
Assert.assertEquals(actual.getChr(), expected.getChr(), "chr");
Assert.assertEquals(actual.getStart(), expected.getStart(), "start");
Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end");
Assert.assertEquals(actual.getID(), expected.getID(), "id");
Assert.assertEquals(
actual.getAlleles(), expected.getAlleles(), "alleles for " + expected + " vs " + actual);
assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(
actual.filtersWereApplied(), expected.filtersWereApplied(), "filtersWereApplied");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "isFiltered");
VariantBaseTest.assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters");
VariantBaseTest.assertEqualsDoubleSmart(
actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
if (expected.hasGenotypes()) {
VariantBaseTest.assertEqualsSet(
actual.getSampleNames(), expected.getSampleNames(), "sample names set");
Assert.assertEquals(
actual.getSampleNamesOrderedByName(),
expected.getSampleNamesOrderedByName(),
"sample names");
final Set<String> samples = expected.getSampleNames();
for (final String sample : samples) {
assertEquals(actual.getGenotype(sample), expected.getGenotype(sample));
}
}
}
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 Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null || !BaseUtils.isRegularBase(ref.getBase())) return 0;
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
for (VariantContext vc : contexts) {
VariantContextBuilder builder = new VariantContextBuilder(vc);
// set the appropriate sample name if necessary
if (sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName())) {
Genotype g =
new GenotypeBuilder(vc.getGenotype(variants.getName())).name(sampleName).make();
builder.genotypes(g);
}
final VariantContext withID = variantOverlapAnnotator.annotateRsID(tracker, builder.make());
writeRecord(withID, tracker, ref.getLocus());
}
return 1;
}
