# Package htsjdk.variant.variantcontext.writer

package htsjdk.variant.variantcontext.writer

Related Packages
Package
Description
htsjdk.variant.variantcontext
htsjdk.variant.variantcontext.filter
Class
Description
AsyncVariantContextWriter
AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.
BCF2Encoder
See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldEncoder
See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldEncoder.AtomicInt
Specialized int encoder for atomic (non-list) integers
BCF2FieldEncoder.Flag
BCF2FieldEncoder.Float
BCF2FieldEncoder.GenericInts
BCF2FieldEncoder.IntArray
BCF2FieldEncoder.StringOrCharacter
BCF2FieldWriter
See #BCFWriter for documentation on this classes role in encoding BCF2 files
BCF2FieldWriter.FTGenotypesWriter
BCF2FieldWriter.GenericSiteWriter
BCF2FieldWriter.GenotypesWriter
BCF2FieldWriter.GTWriter
BCF2FieldWriter.IGFGenotypesWriter
BCF2FieldWriter.IntegerTypeGenotypesWriter
BCF2FieldWriter.SiteWriter
BCF2FieldWriter.StaticallyTypeGenotypesWriter
BCF2FieldWriterManager
See #BCFWriter for documentation on this classes role in encoding BCF2 files
IntGenotypeFieldAccessors
A convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values.
IntGenotypeFieldAccessors.Accessor
IntGenotypeFieldAccessors.ADAccessor
IntGenotypeFieldAccessors.DPAccessor
IntGenotypeFieldAccessors.GQAccessor
IntGenotypeFieldAccessors.PLAccessor
Options
Available writer options for VariantContextWriters
SortingVariantContextWriter
Deprecated.
9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the future
VariantContextWriter
this class writes VCF files
VariantContextWriterBuilder
VariantContextWriterBuilder.OutputType