Package | Description |
---|---|
htsjdk.tribble.index | |
htsjdk.tribble.index.interval | |
htsjdk.tribble.index.linear | |
htsjdk.tribble.index.tabix | |
htsjdk.variant.variantcontext.writer |
Modifier and Type | Class and Description |
---|---|
class |
DynamicIndexCreator
A DynamicIndexCreator creates the proper index based on an
IndexFactory.IndexBalanceApproach and
the characteristics of the file. |
class |
TribbleIndexCreator
Base class for Tribble-specific index creators.
|
Modifier and Type | Method and Description |
---|---|
IndexCreator |
IndexFactory.IndexType.getIndexCreator() |
Modifier and Type | Class and Description |
---|---|
class |
IntervalIndexCreator
Creates interval indexes from a stream of features
|
Modifier and Type | Class and Description |
---|---|
class |
LinearIndexCreator
For creating a LinearIndex from a stream of features.
|
Modifier and Type | Class and Description |
---|---|
class |
TabixIndexCreator
IndexCreator for Tabix.
|
Modifier and Type | Method and Description |
---|---|
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.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,
IndexCreator indexCreator,
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.
|
VariantContextWriterBuilder |
VariantContextWriterBuilder.setIndexCreator(IndexCreator idxCreator)
Set an IndexCreator for the next
VariantContextWriter created by this builder. |