picard.vcf.filter

Class FilterApplyingVariantIterator

java.lang.Object

picard.vcf.filter.FilterApplyingVariantIterator

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

public class FilterApplyingVariantIterator
extends java.lang.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.

Author:

tfennell

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
FilterApplyingVariantIterator(java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> iterator, java.util.Collection<VariantFilter> filters, java.util.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 and 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 Detail

ALL_GTS_FILTERED

public static final java.lang.String ALL_GTS_FILTERED

Filter string that is used to filter a Variant when all variant genotypes are filtered out.

See Also:

Constant Field Values

PASS_FILTER

public static final java.lang.String PASS_FILTER

The "PASS"ing filter String.

See Also:

Constant Field Values

Constructor Detail

FilterApplyingVariantIterator

public FilterApplyingVariantIterator(java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> iterator,
                                     java.util.Collection<VariantFilter> filters,
                                     java.util.Collection<GenotypeFilter> gtFilters)

Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.

Method Detail

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 java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>