htsjdk.variant.variantcontext.writer

Class BCF2FieldWriter

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2FieldWriter

Direct Known Subclasses:

BCF2FieldWriter.GenotypesWriter, BCF2FieldWriter.SiteWriter

public abstract class BCF2FieldWriter
extends java.lang.Object

See #BCFWriter for documentation on this classes role in encoding BCF2 files

Since:

06/12

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BCF2FieldWriter.FTGenotypesWriter
static class	BCF2FieldWriter.GenericSiteWriter
static class	BCF2FieldWriter.GenotypesWriter
static class	BCF2FieldWriter.GTWriter
static class	BCF2FieldWriter.IGFGenotypesWriter
static class	BCF2FieldWriter.IntegerTypeGenotypesWriter
static class	BCF2FieldWriter.SiteWriter
static class	BCF2FieldWriter.StaticallyTypeGenotypesWriter

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	BCF2FieldWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder)

Method Summary

Modifier and Type	Method and Description
void	done(BCF2Encoder encoder, VariantContext vc)
protected java.lang.String	getField()
protected BCF2FieldEncoder	getFieldEncoder()
protected VCFHeader	getHeader()
void	start(BCF2Encoder encoder, VariantContext vc)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BCF2FieldWriter

protected BCF2FieldWriter(VCFHeader header,
                          BCF2FieldEncoder fieldEncoder)

Method Detail

getHeader

protected VCFHeader getHeader()

getFieldEncoder

protected BCF2FieldEncoder getFieldEncoder()

getField

protected java.lang.String getField()

start

public void start(BCF2Encoder encoder,
                  VariantContext vc)
           throws java.io.IOException

Throws:

java.io.IOException

done

public void done(BCF2Encoder encoder,
                 VariantContext vc)
          throws java.io.IOException

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object