picard.vcf.processor

Class VariantIteratorProducer

java.lang.Object

picard.vcf.processor.VariantIteratorProducer

public abstract class VariantIteratorProducer
extends java.lang.Object

A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally an interval list. The produced iterators may perform on-the-fly filtering of the produced VariantContexts.

Author:

mccowan

Constructor Summary

Constructors

Constructor and Description
VariantIteratorProducer()

Method Summary

Modifier and Type	Method and Description
static VariantIteratorProducer	byHundredMegabaseChunks(java.util.List<java.io.File> vcfs) Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
static VariantIteratorProducer	byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(java.util.List<java.io.File> vcfs, htsjdk.samtools.util.IntervalList intervalList) Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of VariantContext
abstract void	close() Closes any latent file handles that may have been opened by calls to iterators().
abstract java.lang.Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>>	iterators() Renders the embodied regions of the VCF files in the form of CloseableIterators over VariantContexts.

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantIteratorProducer

public VariantIteratorProducer()

Method Detail

iterators

public abstract java.lang.Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>> iterators()

Renders the embodied regions of the VCF files in the form of CloseableIterators over VariantContexts. The iterator may perform on-the-fly filtering of these elements.

close

public abstract void close()

Closes any latent file handles that may have been opened by calls to iterators().

byHundredMegabaseChunksWithOnTheFlyFilteringByInterval

public static VariantIteratorProducer byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(java.util.List<java.io.File> vcfs,
                                                                                             htsjdk.samtools.util.IntervalList intervalList)

Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of VariantContext

byHundredMegabaseChunks

public static VariantIteratorProducer byHundredMegabaseChunks(java.util.List<java.io.File> vcfs)

Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).