VariantContextWriterBuilder
@Deprecated
public class VariantContextWriterFactory
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.util.EnumSet<Options> |
DEFAULT_OPTIONS
Deprecated.
|
static java.util.EnumSet<Options> |
NO_OPTIONS
Deprecated.
|
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.
|
public static final java.util.EnumSet<Options> DEFAULT_OPTIONS
public static final java.util.EnumSet<Options> NO_OPTIONS
public static VariantContextWriter create(java.io.File location, SAMSequenceDictionary refDict)
public static VariantContextWriter create(java.io.File location, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
public static VariantContextWriter create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict)
output
- If buffered writing is desired, caller must provide some kind of buffered OutputStream.public static VariantContextWriter create(java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
output
- If buffered writing is desired, caller must provide some kind of buffered OutputStream.public static VariantContextWriter createBcf2(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
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 writtenoutput
- This is where the BCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter createBcf2(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options)
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 writtenoutput
- This is where the BCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter createVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
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 writtenoutput
- This is where the VCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter createVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options)
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 writtenoutput
- This is where the VCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter createBlockCompressedVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
location
- Note that this parameter is used to producing intelligent log messages,
but does not control where the file is writtenoutput
- This is where the VCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter createBlockCompressedVcf(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options)
location
- Note that this parameter is used to producing intelligent log messages,
but does not control where the file is writtenoutput
- This is where the VCF is actually written. If buffered writing is desired, caller must provide
some kind of buffered OutputStream.public static VariantContextWriter create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, java.util.EnumSet<Options> options)
public static VariantContextWriter create(java.io.File location, java.io.OutputStream output, SAMSequenceDictionary refDict, IndexCreator indexCreator, java.util.EnumSet<Options> options)
output
- If buffered writing is desired, caller must provide some kind of buffered OutputStream.public static boolean isBCFOutput(java.io.File location)
location
- public static boolean isBCFOutput(java.io.File location, java.util.EnumSet<Options> options)
public static boolean isCompressedVcf(java.io.File location)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance)
public static VariantContextWriter sortOnTheFly(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
protected static java.io.OutputStream openOutputStream(java.io.File location)
location
-