Package picard.vcf.processor

Class VariantIteratorProducer

java.lang.Object
picard.vcf.processor.VariantIteratorProducer
public abstract class VariantIteratorProducer extends 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.

  • Constructor Details

    • VariantIteratorProducer

      public VariantIteratorProducer()

  • Method Details

    • iterators

      public abstract 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(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

    • 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 of VariantContext

    • 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).

    • byHundredMegabasePathChunks

      public static VariantIteratorProducer byHundredMegabasePathChunks(List<PicardHtsPath> vcfs)
      Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).