Class 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 Detail

      • VariantIteratorProducer

        public VariantIteratorProducer()
    • 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 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
      • 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).