public class VCFRecordCodec extends java.lang.Object implements SortingCollection.Codec<VariantContext>
Constructor and Description |
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VCFRecordCodec(VCFHeader header) |
VCFRecordCodec(VCFHeader header,
boolean allowMissingFieldsInHeader) |
Modifier and Type | Method and Description |
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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.Codec
setOutputStream
in interface SortingCollection.Codec<VariantContext>
public void setInputStream(java.io.InputStream stream)
SortingCollection.Codec
setInputStream
in interface SortingCollection.Codec<VariantContext>
public void encode(VariantContext context)
SortingCollection.Codec
encode
in interface SortingCollection.Codec<VariantContext>
context
- what to writepublic VariantContext decode()
SortingCollection.Codec
decode
in interface SortingCollection.Codec<VariantContext>
public VCFRecordCodec clone()
SortingCollection.Codec
clone
in interface SortingCollection.Codec<VariantContext>
clone
in class java.lang.Object