Package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop

Class SAMRecordReader

java.lang.Object

org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

public class SAMRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class define a RecordReader for SAM files for the Hadoop MapReduce framework.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
SAMRecordReader(org.apache.hadoop.mapreduce.TaskAttemptContext context)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	close()
org.apache.hadoop.io.Text	getCurrentKey()
org.apache.hadoop.io.Text	getCurrentValue()
float	getProgress()
void	initialize(org.apache.hadoop.mapreduce.InputSplit inputSplit, org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Constructor Details

SAMRecordReader

public SAMRecordReader(org.apache.hadoop.mapreduce.TaskAttemptContext context)

Public constructor.

Parameters:

context - the context

Method Details

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

getCurrentKey

public org.apache.hadoop.io.Text getCurrentKey()
                                        throws IOException,
InterruptedException

Specified by:

getCurrentKey in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

getCurrentValue

public org.apache.hadoop.io.Text getCurrentValue()
                                          throws IOException,
InterruptedException

Specified by:

getCurrentValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

getProgress

public float getProgress()
                  throws IOException,
InterruptedException

Specified by:

getProgress in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit inputSplit,
 org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
                throws IOException,
InterruptedException

Specified by:

initialize in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

nextKeyValue

public boolean nextKeyValue()
                     throws IOException,
InterruptedException

Specified by:

nextKeyValue in class org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException