picard.vcf.processor

Class VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>>

java.lang.Object

picard.vcf.processor.VariantProcessor<RESULT,ACCUMULATOR>

public class VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>>
extends java.lang.Object

Describes an object that processes variants and produces a result.

A consumer typically builds an instance of this class via VariantProcessor.Builder, providing it the appropriate VariantProcessor.AccumulatorGenerator and VariantProcessor.ResultMerger, then calls process() to obtain the RESULT of the processing.

Future work...? - Make more efficient for the single-thread case. - A VcfFileSegmentGenerator that is based on an interval list, so that segments' span a constant-size total-base-count overlap with the interval list (or something in that vein).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	VariantProcessor.Accumulator<RESULT> Handles VariantContexts, and accumulates their data in some fashion internally.
static interface	VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> Generates instances of VariantProcessor.Accumulators.
static class	VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,R> Simple builder of VariantProcessors.
static interface	VariantProcessor.ResultMerger<RESULT> Takes a collection of results produced by VariantProcessor.Accumulator.result() and merges them into a single RESULT.

Method Summary

Methods

Modifier and Type	Method and Description
RESULT	process()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

process

public RESULT process()