Package | Description |
---|---|
htsjdk.variant.variantcontext.writer |
Modifier and Type | Field and Description |
---|---|
static java.util.EnumSet<Options> |
VariantContextWriterBuilder.DEFAULT_OPTIONS |
static java.util.EnumSet<Options> |
VariantContextWriterFactory.DEFAULT_OPTIONS
Deprecated.
|
static java.util.EnumSet<Options> |
VariantContextWriterBuilder.NO_OPTIONS |
static java.util.EnumSet<Options> |
VariantContextWriterFactory.NO_OPTIONS
Deprecated.
|
protected java.util.EnumSet<Options> |
VariantContextWriterBuilder.options |
Modifier and Type | Method and Description |
---|---|
static Options |
Options.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static Options[] |
Options.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
static void |
VariantContextWriterBuilder.setDefaultOption(Options option)
Add one option to the set of default
Options that will be used as the initial set of options
for all VariantContextWriterBuilders created after this call. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOption(Options option)
Add one option to the set of
Options for the VariantContextWriterBuilder , if it's not already present. |
static void |
VariantContextWriterBuilder.unsetDefaultOption(Options option)
Remove an option from the set of default
Options that will be used as the initial set of options
for all VariantContextWriterBuilders created after this call. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.unsetOption(Options option)
Remove one option from the set of
Options for the VariantContextWriterBuilder , if it's present. |
Modifier and Type | Method and Description |
---|---|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBcf2(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBcf2(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBlockCompressedVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createBlockCompressedVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
java.util.EnumSet<Options> options)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.createVcf(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict,
IndexCreator indexCreator,
java.util.EnumSet<Options> options)
Deprecated.
|
static boolean |
VariantContextWriterFactory.isBCFOutput(java.io.File location,
java.util.EnumSet<Options> options)
Deprecated.
|
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOptions(java.util.EnumSet<Options> options)
Replace the set of
Options for the VariantContextWriterBuilder with a new set. |