Package picard.sam.markduplicates.util
Class ReadEndsForMarkDuplicatesCodec
- java.lang.Object
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- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
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- All Implemented Interfaces:
htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
,Cloneable
- Direct Known Subclasses:
ReadEndsForMarkDuplicatesWithBarcodesCodec
public class ReadEndsForMarkDuplicatesCodec extends Object implements htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
Codec for ReadEnds that just outputs the primitive fields and reads them back.
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Field Summary
Fields Modifier and Type Field Description protected DataInputStream
in
protected DataOutputStream
out
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Constructor Summary
Constructors Constructor Description ReadEndsForMarkDuplicatesCodec()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
clone()
ReadEndsForMarkDuplicates
decode()
void
encode(ReadEndsForMarkDuplicates read)
DataInputStream
getInputStream()
DataOutputStream
getOutputStream()
void
setInputStream(InputStream is)
void
setOutputStream(OutputStream os)
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Field Detail
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in
protected DataInputStream in
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out
protected DataOutputStream out
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Method Detail
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clone
public htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates> clone()
- Specified by:
clone
in interfacehtsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
- Overrides:
clone
in classObject
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setOutputStream
public void setOutputStream(OutputStream os)
- Specified by:
setOutputStream
in interfacehtsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
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setInputStream
public void setInputStream(InputStream is)
- Specified by:
setInputStream
in interfacehtsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
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getInputStream
public DataInputStream getInputStream()
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getOutputStream
public DataOutputStream getOutputStream()
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encode
public void encode(ReadEndsForMarkDuplicates read)
- Specified by:
encode
in interfacehtsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
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decode
public ReadEndsForMarkDuplicates decode()
- Specified by:
decode
in interfacehtsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>
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