Examples with TargetCollection org.broadinstitute.hellbender.tools.exome.TargetCollection used on opensource projects

Example 16 with TargetCollection

use of org.broadinstitute.hellbender.tools.exome.TargetCollection in project gatk by broadinstitute.

the class EvaluateCopyNumberTriStateCalls method processInterval.

/**
     * Processes a cluster of truth and called variants that may overlap over a genome region.
     * <p>
     * It returns the list of {@link VariantEvaluationContext} instances to be output for the given interval. These
     * are already sorted by coordinates.
     * </p>
     * @param truthReader reader to the truth variants.
     * @param callsReader reader to the called variants.
     * @param interval the interval to analyze.
     * @return never {@code null}.
     */
private List<VariantEvaluationContext> processInterval(final VCFFileReader truthReader, final VCFFileReader callsReader, final SimpleInterval interval, final TargetCollection<Target> targets) {
    final List<VariantContext> truthVariants = variantQueryToList(truthReader, interval);
    final List<VariantContext> callsVariants = variantQueryToList(callsReader, interval);
    final List<VariantEvaluationContext> evaluatedVariants = new ArrayList<>(truthVariants.size() + callsVariants.size());
    for (final VariantContext truth : truthVariants) {
        // skip truth that does not overlap a single target.
        if (targets.targetCount(truth) == 0) {
            continue;
        }
        final List<VariantContext> overlappingCalls = callsVariants.stream().filter(vc -> IntervalUtils.overlaps(truth, vc)).collect(Collectors.toList());
        evaluatedVariants.add(composeTruthOverlappingVariantContext(truth, overlappingCalls, targets));
    }
    for (final VariantContext call : callsVariants) {
        // skip call that does not overlap a single target (the user might want to call on a smaller set of targets)
        if (targets.targetCount(call) == 0) {
            continue;
        }
        final List<VariantContext> overlappingTruth = truthVariants.stream().filter(vc -> IntervalUtils.overlaps(call, vc)).collect(Collectors.toList());
        if (overlappingTruth.isEmpty()) {
            evaluatedVariants.add(composeNonTruthOverlappingVariantContext(call, targets));
        }
    }
    return evaluatedVariants.stream().sorted(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR).map(this::applyVariantContextFilters).collect(Collectors.toList());
}