Examples with HaplotypeCallerEngine org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine used on opensource projects

Example 1 with HaplotypeCallerEngine

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine in project gatk by broadinstitute.

the class HaplotypeCallerSpark method writeVariants.

/**
     * WriteVariants, this is currently going to be horribly slow and explosive on a full size file since it performs a collect.
     *
     * This will be replaced by a parallel writer similar to what's done with {@link org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink}
     */
private void writeVariants(JavaRDD<VariantContext> variants) {
    final List<VariantContext> collectedVariants = variants.collect();
    final SAMSequenceDictionary referenceDictionary = getReferenceSequenceDictionary();
    final List<VariantContext> sortedVariants = collectedVariants.stream().sorted((o1, o2) -> IntervalUtils.compareLocatables(o1, o2, referenceDictionary)).collect(Collectors.toList());
    final HaplotypeCallerEngine hcEngine = new HaplotypeCallerEngine(hcArgs, getHeaderForReads(), new ReferenceMultiSourceAdapter(getReference(), getAuthHolder()));
    try (final VariantContextWriter writer = hcEngine.makeVCFWriter(output, getBestAvailableSequenceDictionary())) {
        hcEngine.writeHeader(writer, getHeaderForReads().getSequenceDictionary(), Collections.emptySet());
        sortedVariants.forEach(writer::add);
    }
}

Example 2 with HaplotypeCallerEngine

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine in project gatk-protected by broadinstitute.

the class HaplotypeCallerSpark method writeVariants.

/**
     * WriteVariants, this is currently going to be horribly slow and explosive on a full size file since it performs a collect.
     *
     * This will be replaced by a parallel writer similar to what's done with {@link org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink}
     */
private void writeVariants(JavaRDD<VariantContext> variants) {
    final List<VariantContext> collectedVariants = variants.collect();
    final SAMSequenceDictionary referenceDictionary = getReferenceSequenceDictionary();
    final List<VariantContext> sortedVariants = collectedVariants.stream().sorted((o1, o2) -> IntervalUtils.compareLocatables(o1, o2, referenceDictionary)).collect(Collectors.toList());
    final HaplotypeCallerEngine hcEngine = new HaplotypeCallerEngine(hcArgs, getHeaderForReads(), new ReferenceMultiSourceAdapter(getReference(), getAuthHolder()));
    try (final VariantContextWriter writer = hcEngine.makeVCFWriter(output, getBestAvailableSequenceDictionary())) {
        hcEngine.writeHeader(writer, getHeaderForReads().getSequenceDictionary(), Collections.emptySet());
        sortedVariants.forEach(writer::add);
    }
}