org.molgenis.vcf

Class VcfReader

java.lang.Object

org.molgenis.vcf.VcfReader

All Implemented Interfaces:

Closeable, AutoCloseable, Iterable<VcfRecord>

public class VcfReader
extends Object
implements Iterable<VcfRecord>, Closeable

A high-performance VCF reader based on the the Variant Call Format (VCF) Version 4.2 Specification

In order to achieve high performance VcfRecord and VcfSample objects are recycled, use createClone() if you need to store these object in a iteration.

Constructor Summary

Constructors

Constructor and Description
VcfReader(net.sf.samtools.util.BlockCompressedInputStream blockCompressedInputStream)
VcfReader(Reader reader)

Method Summary

Modifier and Type	Method and Description
void	close()
VcfMeta	getVcfMeta()
Iterator<VcfRecord>	iterator()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

VcfReader

public VcfReader(Reader reader)

VcfReader

public VcfReader(net.sf.samtools.util.BlockCompressedInputStream blockCompressedInputStream)

Method Detail

iterator

public Iterator<VcfRecord> iterator()

Specified by:

iterator in interface Iterable<VcfRecord>

getVcfMeta

public VcfMeta getVcfMeta()
                   throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException