Package picard.vcf

Class ByIntervalListVariantContextIterator

java.lang.Object
picard.vcf.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 Details

    • 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 Details

    • 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>