picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicatesCodec

java.lang.Object

picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec

All Implemented Interfaces:

htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>, java.lang.Cloneable

Direct Known Subclasses:

ReadEndsForMarkDuplicatesWithBarcodesCodec

public class ReadEndsForMarkDuplicatesCodec
extends java.lang.Object
implements htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>

Codec for ReadEnds that just outputs the primitive fields and reads them back.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.io.DataInputStream	in
protected java.io.DataOutputStream	out

Constructor Summary

Constructors

Constructor and Description
ReadEndsForMarkDuplicatesCodec()

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>	clone()
ReadEndsForMarkDuplicates	decode()
void	encode(ReadEndsForMarkDuplicates read)
java.io.DataInputStream	getInputStream()
java.io.DataOutputStream	getOutputStream()
void	setInputStream(java.io.InputStream is)
void	setOutputStream(java.io.OutputStream os)

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

in

protected java.io.DataInputStream in

out

protected java.io.DataOutputStream out

Constructor Detail

ReadEndsForMarkDuplicatesCodec

public ReadEndsForMarkDuplicatesCodec()

Method Detail

clone

public htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates> clone()

Specified by:

clone in interface htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>

Overrides:

clone in class java.lang.Object

setOutputStream

public void setOutputStream(java.io.OutputStream os)

Specified by:

setOutputStream in interface htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>

setInputStream

public void setInputStream(java.io.InputStream is)

Specified by:

setInputStream in interface htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>

getInputStream

public java.io.DataInputStream getInputStream()

getOutputStream

public java.io.DataOutputStream getOutputStream()

encode

public void encode(ReadEndsForMarkDuplicates read)

Specified by:

encode in interface htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>

decode

public ReadEndsForMarkDuplicates decode()

Specified by:

decode in interface htsjdk.samtools.util.SortingCollection.Codec<ReadEndsForMarkDuplicates>