Package | Description |
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htsjdk.variant.variantcontext.writer |
Modifier and Type | Class and Description |
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class |
AsyncVariantContextWriter
AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.
|
class |
SortingVariantContextWriter
this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)
|
Modifier and Type | Method and Description |
---|---|
VariantContextWriter |
VariantContextWriterBuilder.build()
Validate and build the
VariantContextWriter . |
static VariantContextWriter |
VariantContextWriterFactory.create(java.io.File location,
java.io.OutputStream output,
SAMSequenceDictionary refDict)
Deprecated.
|
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)
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 VariantContextWriter |
VariantContextWriterFactory.sortOnTheFly(VariantContextWriter innerWriter,
int maxCachingStartDistance)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.sortOnTheFly(VariantContextWriter innerWriter,
int maxCachingStartDistance,
boolean takeOwnershipOfInner)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static VariantContextWriter |
VariantContextWriterFactory.sortOnTheFly(VariantContextWriter innerWriter,
int maxCachingStartDistance)
Deprecated.
|
static VariantContextWriter |
VariantContextWriterFactory.sortOnTheFly(VariantContextWriter innerWriter,
int maxCachingStartDistance,
boolean takeOwnershipOfInner)
Deprecated.
|
Constructor and Description |
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AsyncVariantContextWriter(VariantContextWriter out)
Creates a new AsyncVariantContextWriter wrapping the provided VariantContextWriter.
|
AsyncVariantContextWriter(VariantContextWriter out,
int queueSize)
Creates an AsyncVariantContextWriter wrapping the provided VariantContextWriter and using the specified
queue size for buffer VariantContexts.
|
SortingVariantContextWriter(VariantContextWriter innerWriter,
int maxCachingStartDistance) |
SortingVariantContextWriter(VariantContextWriter innerWriter,
int maxCachingStartDistance,
boolean takeOwnershipOfInner)
create a local-sorting VCF writer, given an inner VCF writer to write to
|