htsjdk.variant.variantcontext.writer

Class VariantContextWriterFactory

java.lang.Object

htsjdk.variant.variantcontext.writer.VariantContextWriterFactory

Deprecated.

Replaced by VariantContextWriterBuilder

@Deprecated
public class VariantContextWriterFactory
extends java.lang.Object

Factory methods to create VariantContext writers

Since:

5/12

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.EnumSet<Options>	DEFAULT_OPTIONS Deprecated.
static java.util.EnumSet<Options>	NO_OPTIONS Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
static VariantContextWriter	create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict) Deprecated.
static VariantContextWriter	create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	create(java.io.File location, SAMSequenceDictionary refDict) Deprecated.
static VariantContextWriter	create(java.io.File location, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	create(java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createBcf2(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createBcf2(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createBlockCompressedVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createBlockCompressedVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options) Deprecated.
static VariantContextWriter	createVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options) Deprecated.
static boolean	isBCFOutput(java.io.File location) Deprecated. Should we output a BCF file based solely on the name of the file at location?
static boolean	isBCFOutput(java.io.File location, java.util.EnumSet<Options> options) Deprecated.
static boolean	isCompressedVcf(java.io.File location) Deprecated.
protected static java.io.OutputStream	openOutputStream(java.io.File location) Deprecated. Returns a output stream writing to location, or throws an exception if this fails
static VariantContextWriter	sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance) Deprecated.
static VariantContextWriter	sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner) Deprecated.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_OPTIONS

public static final java.util.EnumSet<Options> DEFAULT_OPTIONS

Deprecated.

NO_OPTIONS

public static final java.util.EnumSet<Options> NO_OPTIONS

Deprecated.

Method Detail

create

public static VariantContextWriter create(java.io.File location,
                          SAMSequenceDictionary refDict)

Deprecated.

create

public static VariantContextWriter create(java.io.File location,
                          SAMSequenceDictionary refDict,
                          java.util.EnumSet<Options> options)

Deprecated.

create

public static VariantContextWriter create(java.io.File location,
                          java.io.OutputStream output,
                          SAMSequenceDictionary refDict)

Deprecated.

Parameters:

output - If buffered writing is desired, caller must provide some kind of buffered OutputStream.

create

public static VariantContextWriter create(java.io.OutputStream output,
                          SAMSequenceDictionary refDict,
                          java.util.EnumSet<Options> options)

Deprecated.

Parameters:

output - If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createBcf2

public static VariantContextWriter createBcf2(java.io.File location,
                              java.io.OutputStream output,
                              SAMSequenceDictionary refDict,
                              java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, and for naming the index, but does not control where the file is written

output - This is where the BCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createBcf2

public static VariantContextWriter createBcf2(java.io.File location,
                              java.io.OutputStream output,
                              SAMSequenceDictionary refDict,
                              IndexCreator indexCreator,
                              java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, and for naming the index, but does not control where the file is written

output - This is where the BCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createVcf

public static VariantContextWriter createVcf(java.io.File location,
                             java.io.OutputStream output,
                             SAMSequenceDictionary refDict,
                             java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, and for naming the index, but does not control where the file is written

output - This is where the VCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createVcf

public static VariantContextWriter createVcf(java.io.File location,
                             java.io.OutputStream output,
                             SAMSequenceDictionary refDict,
                             IndexCreator indexCreator,
                             java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, and for naming the index, but does not control where the file is written

output - This is where the VCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createBlockCompressedVcf

public static VariantContextWriter createBlockCompressedVcf(java.io.File location,
                                            java.io.OutputStream output,
                                            SAMSequenceDictionary refDict,
                                            java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, but does not control where the file is written

output - This is where the VCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

createBlockCompressedVcf

public static VariantContextWriter createBlockCompressedVcf(java.io.File location,
                                            java.io.OutputStream output,
                                            SAMSequenceDictionary refDict,
                                            IndexCreator indexCreator,
                                            java.util.EnumSet<Options> options)

Deprecated.

Parameters:

location - Note that this parameter is used to producing intelligent log messages, but does not control where the file is written

output - This is where the VCF is actually written. If buffered writing is desired, caller must provide some kind of buffered OutputStream.

create

public static VariantContextWriter create(java.io.File location,
                          java.io.OutputStream output,
                          SAMSequenceDictionary refDict,
                          java.util.EnumSet<Options> options)

Deprecated.

create

public static VariantContextWriter create(java.io.File location,
                          java.io.OutputStream output,
                          SAMSequenceDictionary refDict,
                          IndexCreator indexCreator,
                          java.util.EnumSet<Options> options)

Deprecated.

Parameters:

output - If buffered writing is desired, caller must provide some kind of buffered OutputStream.

isBCFOutput

public static boolean isBCFOutput(java.io.File location)

Deprecated.

Should we output a BCF file based solely on the name of the file at location?

Parameters:

location -

Returns:

isBCFOutput

public static boolean isBCFOutput(java.io.File location,
                  java.util.EnumSet<Options> options)

Deprecated.

isCompressedVcf

public static boolean isCompressedVcf(java.io.File location)

Deprecated.

sortOnTheFly

public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter,
                                int maxCachingStartDistance)

Deprecated.

sortOnTheFly

public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter,
                                int maxCachingStartDistance,
                                boolean takeOwnershipOfInner)

Deprecated.

openOutputStream

protected static java.io.OutputStream openOutputStream(java.io.File location)

Deprecated.

Returns a output stream writing to location, or throws an exception if this fails

Parameters:

location -

Returns: