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

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 Details
- VCFRecordCodec
  
  public VCFRecordCodec(VCFHeader header)
- VCFRecordCodec
  
  public VCFRecordCodec(VCFHeader header, boolean allowMissingFieldsInHeader)
Method Details
- 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

Class VCFRecordCodec

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

VCFRecordCodec

VCFRecordCodec

Method Details

setOutputStream

setInputStream

encode

decode

clone