public VariantContextTestData(final VCFHeader header, final List<VariantContext> vcs) {
final Set<String> samples = new HashSet<String>();
for (final VariantContext vc : vcs)
if (vc.hasGenotypes()) samples.addAll(vc.getSampleNames());
this.header =
samples.isEmpty() ? header : new VCFHeader(header.getMetaDataInSortedOrder(), samples);
this.vcs = vcs;
}
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(
actual.getMetaDataInSortedOrder().size(),
expected.getMetaDataInSortedOrder().size(),
"No VCF header lines");
// for some reason set.equals() is returning false but all paired elements are .equals().
// Perhaps compare to is busted?
// Assert.assertEquals(actual.getMetaDataInInputOrder(), expected.getMetaDataInInputOrder());
final List<VCFHeaderLine> actualLines =
new ArrayList<VCFHeaderLine>(actual.getMetaDataInSortedOrder());
final List<VCFHeaderLine> expectedLines =
new ArrayList<VCFHeaderLine>(expected.getMetaDataInSortedOrder());
for (int i = 0; i < actualLines.size(); i++) {
Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
}
}
