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

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

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

Constructor Summary

Constructors

Constructor and Description
ReadEndsForMarkDuplicatesCodec()

Method Summary

Methods

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

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>