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

All Methods Instance Methods Concrete Methods
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 Detail
  - 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:
    
    Constant Field Values
  - PASS_FILTER
```
public static final String PASS_FILTER
```
    The "PASS"ing filter String.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - 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 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 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>

Class FilterApplyingVariantIterator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Field Detail

ALL_GTS_FILTERED

PASS_FILTER

Constructor Detail

FilterApplyingVariantIterator

Method Detail

next

hasNext

close

remove