Package picard.vcf.processor
Class VariantIteratorProducer
java.lang.Object
picard.vcf.processor.VariantIteratorProducer
A mechanism for iterating over
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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
static VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).static VariantIteratorProducer
byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval
(List<PicardHtsPath> 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>>
Renders the embodied regions of the VCF files in the form ofCloseableIterator
s overVariantContext
s.
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Constructor Details
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VariantIteratorProducer
public VariantIteratorProducer()
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Method Details
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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()
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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
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byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval
public static VariantIteratorProducer byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval(List<PicardHtsPath> 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
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byHundredMegabaseChunks
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached). -
byHundredMegabasePathChunks
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
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