Examples with IndexedSampleList org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList used on opensource projects

Example 21 with IndexedSampleList

use of org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList in project gatk-protected by broadinstitute.

the class GenotypeGVCFs method onTraversalStart.

@Override
public void onTraversalStart() {
    final VCFHeader inputVCFHeader = getHeaderForVariants();
    if (onlyOutputCallsStartingInIntervals) {
        if (!hasIntervals()) {
            throw new CommandLineException.MissingArgument("-L or -XL", "Intervals are required if --" + ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME + " was specified.");
        }
    }
    intervals = hasIntervals() ? intervalArgumentCollection.getIntervals(getBestAvailableSequenceDictionary()) : Collections.emptyList();
    //todo should this be getSampleNamesInOrder?
    final SampleList samples = new IndexedSampleList(inputVCFHeader.getGenotypeSamples());
    genotypingEngine = new MinimalGenotypingEngine(createUAC(), samples, new GeneralPloidyFailOverAFCalculatorProvider(genotypeArgs));
    annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbsnp.dbsnp, Collections.emptyList());
    merger = new ReferenceConfidenceVariantContextMerger();
    setupVCFWriter(inputVCFHeader, samples);
}