org.seqdoop.hadoop_bam

Class SAMRecordWritable

java.lang.Object

org.seqdoop.hadoop_bam.SAMRecordWritable

All Implemented Interfaces:

org.apache.hadoop.io.Writable

public class SAMRecordWritable
extends Object
implements org.apache.hadoop.io.Writable

A Writable SAMRecord.

In every mapper, the record will have a header, since BAMInputFormat provides one. It is lost when transferring the SAMRecord to a reducer, however. The current implementation of BAMRecordCodec does not require a record for encoding nor decoding of a SAMRecord, so this fortunately doesn't matter for either write(java.io.DataOutput) or readFields(java.io.DataInput).

Constructor Summary

Constructors

Constructor and Description
SAMRecordWritable()

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.SAMRecord	get()
void	readFields(DataInput in)
void	set(htsjdk.samtools.SAMRecord r)
String	toString()
void	write(DataOutput out)

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMRecordWritable

public SAMRecordWritable()

Method Detail

get

public htsjdk.samtools.SAMRecord get()

set

public void set(htsjdk.samtools.SAMRecord r)

write

public void write(DataOutput out)
           throws IOException

Specified by:

write in interface org.apache.hadoop.io.Writable

Throws:

IOException

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

readFields in interface org.apache.hadoop.io.Writable

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object