de.charite.compbio.jannovar.htsjdk

Class VariantContextWriterConstructionHelper

java.lang.Object

de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper

public final class VariantContextWriterConstructionHelper
extends Object

Helper for creating a VariantContextWriter from a OutputStream. Part of the Jannovar-HTSJDK bridge.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
VariantContextWriterConstructionHelper()

Method Summary

Modifier and Type	Method and Description
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) Forward to openVariantContextWriter(VCFHeader, String, InfoFields, Collection).
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).

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextWriterConstructionHelper

public VariantContextWriterConstructionHelper()

Method Detail

openVariantContextWriter

public 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).

Parameters:

header - the VCF header to use for the construction

outStream - OutputStream to write to

fields - selection of header fields to write out

additionalHeaderLines - additional VCFHeaderLines to add

Returns:

A correct writer for variantContexts

openVariantContextWriter

public 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).

Parameters:

header - the VCF header to use for the construction

fileName - path to output file

fields - selection of header fields to write out

additionalHeaderLines - additional VCFHeaderLines to add

Returns:

A correct writer for variantContexts

openVariantContextWriter

public 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).

Parameters:

header - the VCF header to use for the construction

fileName - path to output file

fields - selection of header fields to write out

additionalHeaderLines - additional VCFHeaderLines to add

generateIndex - whether or not to generate an index

Returns:

A correct writer for variantContexts

openVariantContextWriter

public static htsjdk.variant.variantcontext.writer.VariantContextWriter openVariantContextWriter(htsjdk.variant.vcf.VCFHeader header,
                                                                                                 String fileName,
                                                                                                 InfoFields fields)

Forward to openVariantContextWriter(VCFHeader, String, InfoFields, Collection).

Parameters:

header - the VCF header to use for the construction

fileName - path to output file

fields - selection of header fields to write out

Returns:

A correct writer for variantContexts

extendHeaderFields

public static htsjdk.variant.vcf.VCFHeader extendHeaderFields(htsjdk.variant.vcf.VCFHeader header,
                                                              InfoFields fields)

Extend a VCFHeader with the given fields.

Parameters:

header - the VCFHeader to extend

fields - the InfoFields to get the field selection from

Returns:

extended VCFHeader