@Test
public void testConstructorEmptyGenomes() {
VcfSample sample = new VcfSample("id", (VcfGenome[]) new VcfGenome[0]);
assertNotNull(sample);
assertEquals("id", sample.getId());
assertNotNull(sample.getGenomes());
assertEquals(0, sample.getGenomes().length);
}
@Test
public void testConstructor() {
VcfSample sample = new VcfSample("id", new VcfGenome("genomeId", 1.0d, "Description"));
assertNotNull(sample);
assertEquals("id", sample.getId());
assertNotNull(sample.getGenomes());
assertEquals(1, sample.getGenomes().length);
VcfGenome genome = sample.getGenomes()[0];
assertEquals("genomeId", genome.getId());
assertEquals(1.0d, genome.getMixture(), 0.1d);
assertEquals("Description", genome.getDescription());
}
@Test
public void testBuilder() {
VcfSample sample =
VcfSample.builder()
.withId("id")
.withGenome(new VcfGenome("genomeId", 1.0d, "Description"))
.build();
assertNotNull(sample);
assertEquals("id", sample.getId());
assertNotNull(sample.getGenomes());
assertEquals(1, sample.getGenomes().length);
VcfGenome genome = sample.getGenomes()[0];
assertEquals("genomeId", genome.getId());
assertEquals(1.0d, genome.getMixture(), 0.1d);
assertEquals("Description", genome.getDescription());
}
@Test
public void iteratorSampleMissingValues() throws IOException {
VcfReader vcfReader = new VcfReader(new StringReader(vcfStrSampleMissingValues));
try {
Iterator<VcfRecord> vcfIterator = vcfReader.iterator();
// record 1
if (vcfIterator.hasNext()) {
VcfRecord r = vcfIterator.next();
Iterator<VcfSample> samples = r.getSamples().iterator();
if (samples.hasNext()) {
VcfSample s = samples.next();
assertEquals(s.getAlleles().get(0), Allele.C);
assertEquals(s.getAlleles().get(1), Allele.T);
int idx = r.getFormatIndex("GQ");
assertEquals(s.getData(idx), "12");
}
}
// record 2
if (vcfIterator.hasNext()) {
VcfRecord r = vcfIterator.next();
Iterator<VcfSample> samples = r.getSamples().iterator();
if (samples.hasNext()) {
VcfSample s = samples.next();
assertEquals(s.getAlleles().get(0), Allele.ZERO);
assertEquals(s.getAlleles().get(1), Allele.ZERO);
int idx = r.getFormatIndex("GQ");
assertEquals(s.getData(idx), null);
}
}
} finally {
vcfReader.close();
}
}
