public abstract class VariantIteratorProducer extends Object
CloseableIterator
of VariantContext
s in in some fashion, given VCF files and optionally
an interval list.
The produced iterators may perform on-the-fly filtering of the produced VariantContext
s.Constructor | Description |
---|---|
VariantIteratorProducer() |
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 of
VariantContext |
abstract void |
close() |
Closes any latent file handles that may have been opened by calls to
iterators() . |
abstract Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>> |
iterators() |
Renders the embodied regions of the VCF files in the form of
CloseableIterator s over
VariantContext s. |
public abstract Iterable<htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>> iterators()
CloseableIterator
s over
VariantContext
s. The iterator may perform on-the-fly filtering of these elements.public abstract void close()
iterators()
.public static VariantIteratorProducer byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File> vcfs, htsjdk.samtools.util.IntervalList intervalList)
VariantContext
public static VariantIteratorProducer byHundredMegabaseChunks(List<File> vcfs)