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());
}
}
@Override
public Long map(
final RefMetaDataTracker tracker,
final ReferenceContext ref,
final AlignmentContext context) {
GenomeLoc refLocus = ref.getLocus();
// process and remove any intervals in the map that are don't overlap the current locus anymore
// and add all new intervals that may overlap this reference locus
addNewOverlappingIntervals(refLocus);
outputFinishedIntervals(refLocus, ref.getBase());
// at this point, all intervals in intervalMap overlap with this locus, so update all of them
for (IntervalStratification intervalStratification : intervalMap.values())
intervalStratification.addLocus(context, ref);
return 1L;
}
/**
* Takes the interval, finds it in the stash, prints it to the VCF
*
* @param stats The statistics of the interval
* @param refAllele the reference allele
*/
private void outputStatsToVCF(final IntervalStratification stats, final Allele refAllele) {
GenomeLoc interval = stats.getInterval();
final List<Allele> alleles = new ArrayList<>();
final Map<String, Object> attributes = new HashMap<>();
final ArrayList<Genotype> genotypes = new ArrayList<>();
for (String sample : samples) {
final GenotypeBuilder gb = new GenotypeBuilder(sample);
SampleStratification sampleStat = stats.getSampleStatistics(sample);
gb.attribute(
GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY,
sampleStat.averageCoverage(interval.size()));
gb.attribute(GATKVCFConstants.LOW_COVERAGE_LOCI, sampleStat.getNLowCoveredLoci());
gb.attribute(GATKVCFConstants.ZERO_COVERAGE_LOCI, sampleStat.getNUncoveredLoci());
gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));
genotypes.add(gb.make());
}
alleles.add(refAllele);
alleles.add(SYMBOLIC_ALLELE);
VariantContextBuilder vcb =
new VariantContextBuilder(
"DiagnoseTargets",
interval.getContig(),
interval.getStart(),
interval.getStop(),
alleles);
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR);
vcb.filters(new LinkedHashSet<>(statusToStrings(stats.callableStatuses(), true)));
attributes.put(VCFConstants.END_KEY, interval.getStop());
attributes.put(GATKVCFConstants.AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size()));
attributes.put(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY, stats.gcContent());
vcb = vcb.attributes(attributes);
vcb = vcb.genotypes(genotypes);
vcfWriter.add(vcb.make());
}