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

Class FastqLineRecordReader

java.lang.Object

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

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

All Implemented Interfaces:

Closeable, AutoCloseable

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

Treats keys as offset in file and value as line.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	MAX_LINE_LENGTH

Constructor Summary

Constructors

Constructor	Description
FastqLineRecordReader()
FastqLineRecordReader(byte[] recordDelimiter)

Method Summary

Modifier and Type	Method	Description
void	close()
org.apache.hadoop.io.LongWritable	getCurrentKey()
org.apache.hadoop.io.Text	getCurrentValue()
float	getProgress()	Get the progress within the split
void	initialize(org.apache.hadoop.mapreduce.InputSplit genericSplit, org.apache.hadoop.mapreduce.TaskAttemptContext context)
boolean	nextKeyValue()
boolean	nextKeyValue(boolean cont)

Methods inherited from class java.lang.Object

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

Field Details

MAX_LINE_LENGTH

public static final String MAX_LINE_LENGTH

See Also:

• Constant Field Values

Constructor Details

FastqLineRecordReader

public FastqLineRecordReader()

FastqLineRecordReader

public FastqLineRecordReader(byte[] recordDelimiter)

Method Details

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit genericSplit,
 org.apache.hadoop.mapreduce.TaskAttemptContext context)
                throws IOException

Specified by:

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

Throws:

IOException

nextKeyValue

public boolean nextKeyValue()
                     throws IOException

Specified by:

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

Throws:

IOException

nextKeyValue

public boolean nextKeyValue(boolean cont)
                     throws IOException

Throws:

IOException

getCurrentKey

public org.apache.hadoop.io.LongWritable getCurrentKey()

Specified by:

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

getCurrentValue

public org.apache.hadoop.io.Text getCurrentValue()

Specified by:

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

getProgress

public float getProgress()
                  throws IOException

Get the progress within the split

Specified by:

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

Throws:

IOException

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.LongWritable,org.apache.hadoop.io.Text>

Throws:

IOException