public class VCFRecordCodec extends java.lang.Object implements SortingCollection.Codec<VariantContext>
| Constructor and Description |
|---|
VCFRecordCodec(VCFHeader header) |
VCFRecordCodec(VCFHeader header,
boolean allowMissingFieldsInHeader) |
| Modifier and Type | Method and Description |
|---|---|
VCFRecordCodec |
clone()
Must return a cloned copy of the codec that can be used independently of
the original instance.
|
VariantContext |
decode()
Read the next record from the input stream and convert into a java object.
|
void |
encode(VariantContext context)
Write object to output stream
|
void |
setInputStream(java.io.InputStream stream)
Where to read encoded input from
|
void |
setOutputStream(java.io.OutputStream stream)
Where to write encoded output
|
public VCFRecordCodec(VCFHeader header)
public VCFRecordCodec(VCFHeader header, boolean allowMissingFieldsInHeader)
public void setOutputStream(java.io.OutputStream stream)
SortingCollection.CodecsetOutputStream in interface SortingCollection.Codec<VariantContext>public void setInputStream(java.io.InputStream stream)
SortingCollection.CodecsetInputStream in interface SortingCollection.Codec<VariantContext>public void encode(VariantContext context)
SortingCollection.Codecencode in interface SortingCollection.Codec<VariantContext>context - what to writepublic VariantContext decode()
SortingCollection.Codecdecode in interface SortingCollection.Codec<VariantContext>public VCFRecordCodec clone()
SortingCollection.Codecclone in interface SortingCollection.Codec<VariantContext>clone in class java.lang.Object