Package picard.vcf.processor
Class VariantIteratorProducer
- java.lang.Object
-
- picard.vcf.processor.VariantIteratorProducer
-
public abstract class VariantIteratorProducer extends Object
A mechanism for iterating overCloseableIterator
ofVariantContext
s in in some fashion, given VCF files and optionally an interval list. The produced iterators may perform on-the-fly filtering of the producedVariantContext
s.
-
-
Constructor Summary
Constructors Constructor Description VariantIteratorProducer()
-
Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description static VariantIteratorProducer
byHundredMegabaseChunks(List<File> vcfs)
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).static VariantIteratorProducer
byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<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 ofVariantContext
abstract void
close()
Closes any latent file handles that may have been opened by calls toiterators()
.abstract Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>>
iterators()
Renders the embodied regions of the VCF files in the form ofCloseableIterator
s overVariantContext
s.
-
-
-
Method Detail
-
iterators
public abstract Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>> iterators()
Renders the embodied regions of the VCF files in the form ofCloseableIterator
s overVariantContext
s. 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 toiterators()
.
-
byHundredMegabaseChunksWithOnTheFlyFilteringByInterval
public static VariantIteratorProducer byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<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 ofVariantContext
-
byHundredMegabaseChunks
public static VariantIteratorProducer byHundredMegabaseChunks(List<File> vcfs)
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
-
-