Package | Description |
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htsjdk.variant.variantcontext.writer |
Modifier and Type | Method and Description |
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void |
BCF2FieldWriter.GenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.IGFGenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.FTGenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.GTWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.done(BCF2Encoder encoder,
VariantContext vc) |
abstract void |
BCF2FieldEncoder.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues)
Key abstract method that should encode a value of the given type into the encoder.
|
void |
BCF2FieldEncoder.StringOrCharacter.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.Flag.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.Float.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.IntArray.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.AtomicInt.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.GenericInts.encodeValue(BCF2Encoder encoder,
Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldWriterManager.setup(VCFHeader header,
BCF2Encoder encoder,
Map<String,Integer> stringDictionary)
Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header
Must be called before any of the getter methods will work
|
abstract void |
BCF2FieldWriter.SiteWriter.site(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GenericSiteWriter.site(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.IntegerTypeGenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.IGFGenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GTWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldEncoder.writeFieldKey(BCF2Encoder encoder)
Write the field key (dictionary offset and type) into the BCF2Encoder stream
|