/**
* 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));
}
}
}
private VariantContext getDbsnp(String rsID) {
if (dbsnpIterator == null) {
if (dbsnp == null)
throw new UserException.BadInput(
"No dbSNP rod was provided, but one is needed to decipher the correct indel alleles from the HapMap records");
RMDTrackBuilder builder =
new RMDTrackBuilder(
getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),
getToolkit().getGenomeLocParser(),
getToolkit().getArguments().unsafe,
getToolkit().getArguments().disableAutoIndexCreationAndLockingWhenReadingRods,
null);
dbsnpIterator =
builder
.createInstanceOfTrack(VCFCodec.class, new File(dbsnp.dbsnp.getSource()))
.getIterator();
// Note that we should really use some sort of seekable iterator here so that the search
// doesn't take forever
// (but it's complicated because the hapmap location doesn't match the dbsnp location, so we
// don't know where to seek to)
}
while (dbsnpIterator.hasNext()) {
GATKFeature feature = dbsnpIterator.next();
VariantContext vc = (VariantContext) feature.getUnderlyingObject();
if (vc.getID().equals(rsID)) return vc;
}
return null;
}