Package picard.vcf.processor
-
Interface Summary Interface Description VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> Describes the functionality for an executor that manages the delegation of work toVariantProcessor.Accumulators.VariantProcessor.Accumulator<RESULT> HandlesVariantContexts, and accumulates their data in some fashion internally.VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> Generates instances ofVariantProcessor.Accumulators.VariantProcessor.ResultMerger<RESULT> Takes a collection of results produced byVariantProcessor.Accumulator.result()and merges them into a single RESULT. -
Class Summary Class Description VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,R> AVariantAccumulatorExecutorthat breaks down work into chunks described by the providedVariantIteratorProducerand spreads them over the indicated number of threads.VariantIteratorProducer A mechanism for iterating overCloseableIteratorofVariantContexts in in some fashion, given VCF files and optionally an interval list.VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> Describes an object that processes variants and produces a result.VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,R> Simple builder ofVariantProcessors.VcfFileSegment Describes a segment of a particular VCF file.VcfFileSegmentGenerator Describes a mechanism for producingVcfFileSegments from a VCF file.