Class FilterApplyingVariantIterator

java.lang.Object
picard.vcf.filter.FilterApplyingVariantIterator
All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>, Closeable, AutoCloseable, Iterator<htsjdk.variant.variantcontext.VariantContext>
public class FilterApplyingVariantIterator extends Object implements htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator. Returns all records from the underlying stream and does not remove any.

  • Field Details

    • ALL_GTS_FILTERED

      public static final String ALL_GTS_FILTERED
      Filter string that is used to filter a Variant when all variant genotypes are filtered out.
      See Also:

    • PASS_FILTER

      public static final String PASS_FILTER
      The "PASS"ing filter String.
      See Also:

  • Constructor Details

    • FilterApplyingVariantIterator

      public FilterApplyingVariantIterator(Iterator<htsjdk.variant.variantcontext.VariantContext> iterator, Collection<VariantFilter> filters, Collection<GenotypeFilter> gtFilters)
      Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.

  • Method Details

    • next

      public htsjdk.variant.variantcontext.VariantContext next()
      Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
      Specified by:
      next in interface Iterator<htsjdk.variant.variantcontext.VariantContext>

    • hasNext

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

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>

    • remove

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