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.
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionFilterApplyingVariantIterator
(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
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
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Field Details
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ALL_GTS_FILTERED
Filter string that is used to filter a Variant when all variant genotypes are filtered out.- See Also:
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PASS_FILTER
The "PASS"ing filter String.- See Also:
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Constructor Details
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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.
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Method Details
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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. -
hasNext
public boolean hasNext() -
close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfacehtsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>
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remove
public void remove()
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