Package picard.vcf.filter

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 Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    ALL_GTS_FILTERED
    Filter string that is used to filter a Variant when all variant genotypes are filtered out.
    static final String
    PASS_FILTER
    The "PASS"ing filter String.

  • Constructor Summary

    Constructors
    Constructor
    Description
    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 Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    boolean
    hasNext()
     
    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.
    void
    remove()
     

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface htsjdk.samtools.util.CloseableIterator

    stream, toList

    Methods inherited from interface java.util.Iterator

    forEachRemaining

  • 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>