Package picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicatesCodec

java.lang.Object

picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec

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.

Field Summary

Fields

Modifier and Type	Field	Description
protected DataInputStream	in
protected DataOutputStream	out

Constructor Summary

Constructors

Constructor	Description
ReadEndsForMarkDuplicatesCodec()

Method Summary

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)

Methods inherited from class java.lang.Object

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

Field Details

in

protected DataInputStream in

out

protected DataOutputStream out

Constructor Details

ReadEndsForMarkDuplicatesCodec

public ReadEndsForMarkDuplicatesCodec()

Method Details

clone

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

Specified by:

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

Overrides:

clone in class Object

setOutputStream

public void setOutputStream(OutputStream os)

Specified by:

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

setInputStream

public void setInputStream(InputStream is)

Specified by:

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

getInputStream

public DataInputStream getInputStream()

getOutputStream

public 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>