java.lang.Object
- htsjdk.variant.vcf.VCFRecordCodec

All Implemented Interfaces:

SortingCollection.Codec<VariantContext>, Cloneable
```
public class VCFRecordCodec
extends Object
implements SortingCollection.Codec<VariantContext>
```
Writes VariantContext instances to an OutputStream without headers or metadata. For use with SortingCollection ONLY.

Constructor Summary

Constructors
Constructor Description

VCFRecordCodec(VCFHeader header)

VCFRecordCodec(VCFHeader header, boolean allowMissingFieldsInHeader)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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(InputStream stream)`	Where to read encoded input from
`void`	`setOutputStream(OutputStream stream)`	Where to write encoded output

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - VCFRecordCodec
```
public VCFRecordCodec(VCFHeader header)
```
  - VCFRecordCodec
```
public VCFRecordCodec(VCFHeader header,
                      boolean allowMissingFieldsInHeader)
```
- Method Detail
  - setOutputStream
```
public void setOutputStream(OutputStream stream)
```
    Description copied from interface: SortingCollection.Codec
    
    Where to write encoded output
    
    Specified by:
    
    setOutputStream in interface SortingCollection.Codec<VariantContext>
  - setInputStream
```
public void setInputStream(InputStream stream)
```
    Description copied from interface: SortingCollection.Codec
    
    Where to read encoded input from
    
    Specified by:
    
    setInputStream in interface SortingCollection.Codec<VariantContext>
  - encode
```
public void encode(VariantContext context)
```
    Description copied from interface: SortingCollection.Codec
    
    Write object to output stream
    
    Specified by:
    
    encode in interface SortingCollection.Codec<VariantContext>
    
    Parameters:
    
    context - what to write
  - decode
```
public VariantContext decode()
```
    Description copied from interface: SortingCollection.Codec
    
    Read the next record from the input stream and convert into a java object.
    
    Specified by:
    
    decode in interface SortingCollection.Codec<VariantContext>
    
    Returns:
    
    null if no more records. Should throw exception if EOF is encountered in the middle of a record.
  - clone
```
public VCFRecordCodec clone()
```
    Description copied from interface: SortingCollection.Codec
    
    Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.
    
    Specified by:
    
    clone in interface SortingCollection.Codec<VariantContext>
    
    Overrides:
    
    clone in class Object

Constructor	Description
`VCFRecordCodec(VCFHeader header)`
`VCFRecordCodec(VCFHeader header, boolean allowMissingFieldsInHeader)`

Class VCFRecordCodec

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

VCFRecordCodec

VCFRecordCodec

Method Detail

setOutputStream

setInputStream

encode

decode

clone