htsjdk.variant.vcf

Interface VCFIterator

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, CloseableIterator<VariantContext>, java.util.Iterator<VariantContext>

public interface VCFIterator
extends CloseableIterator<VariantContext>

An iterator of `VariantContext`. This iterator can be used to decode VCF data on the fly . Example:

 VCFIterator r = new VCFIteratorBuilder().open(System.in);
 while (r.hasNext()) {
     System.out.println(r.next());
 }
 r.close();
 

See Also:

VCFIteratorBuilder

Method Summary

Modifier and Type	Method and Description
VCFHeader	getHeader() Returns the VCFHeader associated with this VCF/BCF file.
VariantContext	peek() Returns the next object but does not advance the iterator.

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

close, stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next, remove

Method Detail

getHeader

VCFHeader getHeader()

Returns the VCFHeader associated with this VCF/BCF file.

peek

VariantContext peek()

Returns the next object but does not advance the iterator. Subsequent calls to peek() and next() will return the same object.