Package htsjdk.variant.vcf
Class VCFIteratorBuilder
- java.lang.Object
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- htsjdk.variant.vcf.VCFIteratorBuilder
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public class VCFIteratorBuilder extends Object
A Class buildingVCFIterator
Example:VCFIterator r = new VCFIteratorBuilder().open(System.in); while (r.hasNext()) { System.out.println(r.next()); } r.close();
- See Also:
VCFIterator
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Constructor Summary
Constructors Constructor Description VCFIteratorBuilder()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description VCFIterator
open(File file)
creates a VCF iterator from a FileVCFIterator
open(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(String path)
creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.VCFIterator
open(String path, Function<SeekableByteChannel,SeekableByteChannel> wrapper)
creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.VCFIterator
open(Path path)
creates a VCF iterator from a PathVCFIterator
open(Path path, Function<SeekableByteChannel,SeekableByteChannel> wrapper)
creates a VCF iterator from a Path
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Method Detail
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open
public VCFIterator open(InputStream in) throws 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:
IOException
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open
public VCFIterator open(String path) throws 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:
IOException
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open
public VCFIterator open(Path path) throws IOException
creates a VCF iterator from a Path- Parameters:
path
- the path- Returns:
- the VCFIterator
- Throws:
IOException
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open
public VCFIterator open(Path path, Function<SeekableByteChannel,SeekableByteChannel> wrapper) throws IOException
creates a VCF iterator from a Path- Parameters:
path
- the file pathwrapper
- wrapper forSeekablePathStream
. Can be null.- Returns:
- the VCFIterator
- Throws:
IOException
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open
public VCFIterator open(String path, Function<SeekableByteChannel,SeekableByteChannel> wrapper) throws IOException
creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.- Parameters:
path
- the Pathwrapper
- wrapper forSeekablePathStream
. Can be null.- Returns:
- the VCFIterator
- Throws:
IOException
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open
public VCFIterator open(File file) throws IOException
creates a VCF iterator from a File- Parameters:
file
- the file (can be bcf, vcf, vcf.gz)- Returns:
- the VCFIterator
- Throws:
IOException
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