private void outputMissingInterval(final IntervalStratification stats) {
final GenomeLoc interval = stats.getInterval();
final boolean missing[] = new boolean[interval.size()];
Arrays.fill(missing, true);
for (AbstractStratification sample : stats.getElements()) {
if (hasMissingStatuses(sample)) {
int pos = 0;
for (AbstractStratification locus : sample.getElements()) {
if (locus.callableStatuses().isEmpty()) {
missing[pos] = false;
}
pos++;
}
}
}
int start = -1;
boolean insideMissing = false;
for (int i = 0; i < missing.length; i++) {
if (missing[i] && !insideMissing) {
start = interval.getStart() + i;
insideMissing = true;
} else if (!missing[i] && insideMissing) {
final int stop = interval.getStart() + i - 1;
outputMissingInterval(interval.getContig(), start, stop);
insideMissing = false;
}
}
if (insideMissing) {
outputMissingInterval(interval.getContig(), start, interval.getStop());
}
}
@Test
public void testFixReverseComplementedGenotypes() {
final Allele refA = Allele.create("A", true);
final Allele altC = Allele.create("C", false);
final GenotypesContext originalGenotypes = GenotypesContext.create(3);
originalGenotypes.add(new GenotypeBuilder("homref").alleles(Arrays.asList(refA, refA)).make());
originalGenotypes.add(new GenotypeBuilder("het").alleles(Arrays.asList(refA, altC)).make());
originalGenotypes.add(new GenotypeBuilder("homvar").alleles(Arrays.asList(altC, altC)).make());
final Allele refT = Allele.create("T", true);
final Allele altG = Allele.create("G", false);
final GenotypesContext expectedGenotypes = GenotypesContext.create(3);
expectedGenotypes.add(new GenotypeBuilder("homref").alleles(Arrays.asList(refT, refT)).make());
expectedGenotypes.add(new GenotypeBuilder("het").alleles(Arrays.asList(refT, altG)).make());
expectedGenotypes.add(new GenotypeBuilder("homvar").alleles(Arrays.asList(altG, altG)).make());
final Map<Allele, Allele> reverseComplementAlleleMap = new HashMap<Allele, Allele>(2);
reverseComplementAlleleMap.put(refA, refT);
reverseComplementAlleleMap.put(altC, altG);
final GenotypesContext actualGenotypes =
LiftoverVcf.fixGenotypes(originalGenotypes, reverseComplementAlleleMap);
for (final String sample : Arrays.asList("homref", "het", "homvar")) {
final List<Allele> expected = expectedGenotypes.get(sample).getAlleles();
final List<Allele> actual = actualGenotypes.get(sample).getAlleles();
Assert.assertEquals(expected.get(0), actual.get(0));
Assert.assertEquals(expected.get(1), actual.get(1));
}
}
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);
}