htsjdk.variant.vcf

Class VCFIteratorBuilder

java.lang.Object

htsjdk.variant.vcf.VCFIteratorBuilder

public class VCFIteratorBuilder
extends java.lang.Object

A Class building VCFIterator Example:

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

See Also:

VCFIterator

Constructor Summary

Constructors

Constructor and Description
VCFIteratorBuilder()

Method Summary

Modifier and Type	Method and Description
VCFIterator	open(java.io.File file) creates a VCF iterator from a File
VCFIterator	open(java.io.InputStream in) creates a VCF iterator from an input stream It detects if the stream is a BCF stream or a GZipped stream.
VCFIterator	open(java.nio.file.Path path) creates a VCF iterator from a Path
VCFIterator	open(java.nio.file.Path path, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper) creates a VCF iterator from a Path
VCFIterator	open(java.lang.String path) creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.
VCFIterator	open(java.lang.String path, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper) creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFIteratorBuilder

public VCFIteratorBuilder()

Method Detail

open

public VCFIterator open(java.io.InputStream in)
                 throws java.io.IOException

creates a VCF iterator from an input stream It detects if the stream is a BCF stream or a GZipped stream.

Parameters:

in - inputstream

Returns:

the VCFIterator

Throws:

java.io.IOException

open

public VCFIterator open(java.lang.String path)
                 throws java.io.IOException

creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.

Parameters:

path - the Path

Returns:

the VCFIterator

Throws:

java.io.IOException

open

public VCFIterator open(java.nio.file.Path path)
                 throws java.io.IOException

creates a VCF iterator from a Path

Parameters:

path - the path

Returns:

the VCFIterator

Throws:

java.io.IOException

open

public VCFIterator open(java.nio.file.Path path,
                        java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper)
                 throws java.io.IOException

creates a VCF iterator from a Path

Parameters:

path - the file path

wrapper - wrapper for SeekablePathStream. Can be null.

Returns:

the VCFIterator

Throws:

java.io.IOException

open

public VCFIterator open(java.lang.String path,
                        java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper)
                 throws java.io.IOException

creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.

Parameters:

path - the Path

wrapper - wrapper for SeekablePathStream. Can be null.

Returns:

the VCFIterator

Throws:

java.io.IOException

open

public VCFIterator open(java.io.File file)
                 throws java.io.IOException

creates a VCF iterator from a File

Parameters:

file - the file (can be bcf, vcf, vcf.gz)

Returns:

the VCFIterator

Throws:

java.io.IOException