/**
* Function that process a set of statuses into strings
*
* @param statuses the set of statuses to be converted
* @return a matching set of strings
*/
private List<String> statusToStrings(
Iterable<CallableStatus> statuses, final boolean isInfoField) {
List<String> output = new LinkedList<>();
for (CallableStatus status : statuses)
if (isInfoField || status != CallableStatus.PASS) output.add(status.name());
return output;
}
/**
* 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());
}
/**
* Outputs all intervals that are behind the current reference locus
*
* @param refLocus the current reference locus
* @param refBase the reference allele
*/
private void outputFinishedIntervals(final GenomeLoc refLocus, final byte refBase) {
// output any intervals that were finished
final List<GenomeLoc> toRemove = new LinkedList<>();
for (GenomeLoc key : intervalMap.keySet()) {
if (key.isBefore(refLocus)) {
final IntervalStratification intervalStats = intervalMap.get(key);
outputStatsToVCF(intervalStats, Allele.create(refBase, true));
if (hasMissingLoci(intervalStats)) {
outputMissingInterval(intervalStats);
}
toRemove.add(key);
}
}
for (GenomeLoc key : toRemove) {
intervalMap.remove(key);
}
}