Package picard.vcf

Class ByIntervalListVariantContextIterator

  • All Implemented Interfaces:
    Iterator<htsjdk.variant.variantcontext.VariantContext>

    public class ByIntervalListVariantContextIterator
    extends Object
    implements Iterator<htsjdk.variant.variantcontext.VariantContext>
    Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals. //TODO Currently this uses the VCFFileReader.query method - could be useful to make a version of this iterator that uses the .iterator method
    • Constructor Detail

      • ByIntervalListVariantContextIterator

        public ByIntervalListVariantContextIterator​(htsjdk.variant.vcf.VCFFileReader reader,
                                                    htsjdk.samtools.util.IntervalList intervals)
        Parameters:
        reader - the source of variants.
        intervals - the intervals to which to restrict variants.
    • Method Detail

      • hasNext

        public boolean hasNext()
        Specified by:
        hasNext in interface Iterator<htsjdk.variant.variantcontext.VariantContext>
      • next

        public htsjdk.variant.variantcontext.VariantContext next()
        Specified by:
        next in interface Iterator<htsjdk.variant.variantcontext.VariantContext>
      • remove

        public void remove()
        Specified by:
        remove in interface Iterator<htsjdk.variant.variantcontext.VariantContext>