Class VCFIteratorBuilder
java.lang.Object
htsjdk.variant.vcf.VCFIteratorBuilder
A Class building
VCFIterator
Example:
VCFIterator r = new VCFIteratorBuilder().open(System.in);
while (r.hasNext()) {
System.out.println(r.next());
}
r.close();
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncreates a VCF iterator from a Fileopen(InputStream in) creates a VCF iterator from an input stream It detects if the stream is a BCF stream or a GZipped stream.creates a VCF iterator from a URI It detects if the stream is a BCF stream or a GZipped stream.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.creates a VCF iterator from a Pathopen(Path path, Function<SeekableByteChannel, SeekableByteChannel> wrapper) creates a VCF iterator from a Path
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Constructor Details
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VCFIteratorBuilder
public VCFIteratorBuilder()
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Method Details
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open
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
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
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
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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