public final class VariantContextWriterConstructionHelper extends Object
VariantContextWriter
from a OutputStream
.
Part of the Jannovar-HTSJDK bridge.Constructor and Description |
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VariantContextWriterConstructionHelper() |
Modifier and Type | Method and Description |
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static htsjdk.variant.vcf.VCFHeader |
extendHeaderFields(htsjdk.variant.vcf.VCFHeader header,
InfoFields fields)
Extend a
VCFHeader with the given fields . |
static htsjdk.variant.variantcontext.writer.VariantContextWriter |
openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header,
OutputStream outStream,
InfoFields fields,
Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines)
Return a new
VariantContextWriter that uses the header from reader but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields) . |
static htsjdk.variant.variantcontext.writer.VariantContextWriter |
openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header,
String fileName,
InfoFields fields)
|
static htsjdk.variant.variantcontext.writer.VariantContextWriter |
openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header,
String fileName,
InfoFields fields,
Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines)
Return a new
VariantContextWriter that uses the header from reader but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields) . |
static htsjdk.variant.variantcontext.writer.VariantContextWriter |
openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header,
String fileName,
InfoFields fields,
Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines,
boolean generateIndex)
Return a new
VariantContextWriter that uses the header from reader but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields) . |
public VariantContextWriterConstructionHelper()
public static htsjdk.variant.variantcontext.writer.VariantContextWriter openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header, OutputStream outStream, InfoFields fields, Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines)
VariantContextWriter
that uses the header from reader
but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields)
.header
- the VCF header to use for the constructionoutStream
- OutputStream
to write tofields
- selection of header fields to write outadditionalHeaderLines
- additional VCFHeaderLine
s to addpublic static htsjdk.variant.variantcontext.writer.VariantContextWriter openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header, String fileName, InfoFields fields, Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines)
VariantContextWriter
that uses the header from reader
but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields)
.header
- the VCF header to use for the constructionfileName
- path to output filefields
- selection of header fields to write outadditionalHeaderLines
- additional VCFHeaderLine
s to addpublic static htsjdk.variant.variantcontext.writer.VariantContextWriter openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header, String fileName, InfoFields fields, Collection<htsjdk.variant.vcf.VCFHeaderLine> additionalHeaderLines, boolean generateIndex)
VariantContextWriter
that uses the header from reader
but has the header
extended header through extendHeaderFields(htsjdk.variant.vcf.VCFHeader, de.charite.compbio.jannovar.htsjdk.InfoFields)
.header
- the VCF header to use for the constructionfileName
- path to output filefields
- selection of header fields to write outadditionalHeaderLines
- additional VCFHeaderLine
s to addgenerateIndex
- whether or not to generate an indexpublic static htsjdk.variant.variantcontext.writer.VariantContextWriter openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header, String fileName, InfoFields fields)
header
- the VCF header to use for the constructionfileName
- path to output filefields
- selection of header fields to write outpublic static htsjdk.variant.vcf.VCFHeader extendHeaderFields(htsjdk.variant.vcf.VCFHeader header, InfoFields fields)
VCFHeader
with the given fields
.header
- the VCFHeader
to extendfields
- the InfoFields
to get the field selection fromCopyright © 2016. All rights reserved.