htsjdk.variant.vcf

Interface VCFReader

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, java.lang.Iterable<VariantContext>

All Known Implementing Classes:

VCFFileReader

public interface VCFReader
extends java.io.Closeable, java.lang.Iterable<VariantContext>

Interface for reading VCF/BCF files.

Method Summary

Modifier and Type	Method and Description
VCFHeader	getHeader() Returns the VCFHeader associated with this VCFReader.
boolean	isQueryable() A method to check if the reader is query-able, i.e.
CloseableIterator<VariantContext>	iterator()
default CloseableIterator<VariantContext>	query(Locatable locatable) Queries for records overlapping the Locatable specified.
CloseableIterator<VariantContext>	query(java.lang.String chrom, int start, int end) Queries for records overlapping the region specified.

Methods inherited from interface java.io.Closeable

close

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Method Detail

getHeader

VCFHeader getHeader()

Returns the VCFHeader associated with this VCFReader.

query

CloseableIterator<VariantContext> query(java.lang.String chrom,
                                        int start,
                                        int end)

Queries for records overlapping the region specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.

Parameters:

chrom - the chomosome to query

start - query interval start

end - query interval end

Returns:

non-null iterator over VariantContexts

query

default CloseableIterator<VariantContext> query(Locatable locatable)

Queries for records overlapping the Locatable specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.

Returns:

non-null iterator over VariantContexts

isQueryable

boolean isQueryable()

A method to check if the reader is query-able, i.e. if a call to VCFFileReader.query(String, int, int) can be successful

Returns:

true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.

iterator

CloseableIterator<VariantContext> iterator()

Specified by:

iterator in interface java.lang.Iterable<VariantContext>