/**
* 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 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;
}
private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, GenomeLoc loc) {
if (!wroteHeader) {
wroteHeader = true;
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for (VCFHeaderLine field : hInfo) {
if (field instanceof VCFFormatHeaderLine) {
allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine) field).getID());
}
}
samples = new LinkedHashSet<String>();
if (sampleName != null) {
samples.add(sampleName);
} else {
// try VCF first
samples =
SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
if (samples.isEmpty()) {
List<Feature> features = tracker.getValues(variants, loc);
if (features.size() == 0)
throw new IllegalStateException(
"No rod data is present, but we just created a VariantContext");
Feature f = features.get(0);
if (f instanceof RawHapMapFeature)
samples.addAll(Arrays.asList(((RawHapMapFeature) f).getSampleIDs()));
else samples.addAll(vc.getSampleNames());
}
}
vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
}
vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
vcfwriter.add(vc);
}