Package htsjdk.variant.vcf
Class VCFRecordCodec
- java.lang.Object
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- htsjdk.variant.vcf.VCFRecordCodec
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- 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.
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Constructor Summary
Constructors Constructor Description VCFRecordCodec(VCFHeader header)
VCFRecordCodec(VCFHeader header, boolean allowMissingFieldsInHeader)
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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 streamvoid
setInputStream(InputStream stream)
Where to read encoded input fromvoid
setOutputStream(OutputStream stream)
Where to write encoded output
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Method Detail
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setOutputStream
public void setOutputStream(OutputStream stream)
Description copied from interface:SortingCollection.Codec
Where to write encoded output- Specified by:
setOutputStream
in interfaceSortingCollection.Codec<VariantContext>
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setInputStream
public void setInputStream(InputStream stream)
Description copied from interface:SortingCollection.Codec
Where to read encoded input from- Specified by:
setInputStream
in interfaceSortingCollection.Codec<VariantContext>
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encode
public void encode(VariantContext context)
Description copied from interface:SortingCollection.Codec
Write object to output stream- Specified by:
encode
in interfaceSortingCollection.Codec<VariantContext>
- Parameters:
context
- what to write
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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 interfaceSortingCollection.Codec<VariantContext>
- Returns:
- null if no more records. Should throw exception if EOF is encountered in the middle of a record.
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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 interfaceSortingCollection.Codec<VariantContext>
- Overrides:
clone
in classObject
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