org.bdgenomics.adam.io

Class InterleavedFastqInputFormat.InterleavedFastqRecordReader

java.lang.Object

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

org.bdgenomics.adam.io.InterleavedFastqInputFormat.InterleavedFastqRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

Enclosing class:

InterleavedFastqInputFormat

public static class InterleavedFastqInputFormat.InterleavedFastqRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<Void,org.apache.hadoop.io.Text>

Constructor Summary

Constructors

Constructor and Description
InterleavedFastqRecordReader(org.apache.hadoop.conf.Configuration conf, org.apache.hadoop.mapreduce.lib.input.FileSplit split)

Method Summary

Modifier and Type	Method and Description
void	close() Close this RecordReader to future operations.
org.apache.hadoop.io.Text	createKey() Create an object of the appropriate type to be used as a key.
org.apache.hadoop.io.Text	createValue() Create an object of the appropriate type to be used as a value.
Void	getCurrentKey() Added to use mapreduce API.
org.apache.hadoop.io.Text	getCurrentValue() Added to use mapreduce API.
long	getPos() Returns the current position in the input.
float	getProgress() How much of the input has the RecordReader consumed i.e.
void	initialize(org.apache.hadoop.mapreduce.InputSplit split, org.apache.hadoop.mapreduce.TaskAttemptContext context) Added to use mapreduce API.
protected boolean	lowLevelFastqRead(org.apache.hadoop.io.Text readName, org.apache.hadoop.io.Text value)
String	makePositionMessage()
boolean	next(org.apache.hadoop.io.Text value) Reads the next key/value pair from the input for processing.
boolean	nextKeyValue() Added to use mapreduce API.

Methods inherited from class java.lang.Object

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

Constructor Detail

InterleavedFastqRecordReader

public InterleavedFastqRecordReader(org.apache.hadoop.conf.Configuration conf,
                                    org.apache.hadoop.mapreduce.lib.input.FileSplit split)
                             throws IOException

Throws:

IOException

Method Detail

initialize

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

Added to use mapreduce API.

Specified by:

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

Throws:

IOException

InterruptedException

getCurrentKey

public Void getCurrentKey()

Added to use mapreduce API.

Specified by:

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

getCurrentValue

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

Added to use mapreduce API.

Specified by:

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

nextKeyValue

public boolean nextKeyValue()
                     throws IOException,
                            InterruptedException

Added to use mapreduce API.

Specified by:

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

Throws:

IOException

InterruptedException

close

public void close()
           throws IOException

Close this RecordReader to future operations.

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

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

Throws:

IOException

createKey

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

Create an object of the appropriate type to be used as a key.

createValue

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

Create an object of the appropriate type to be used as a value.

getPos

public long getPos()

Returns the current position in the input.

getProgress

public float getProgress()

How much of the input has the RecordReader consumed i.e.

Specified by:

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

makePositionMessage

public String makePositionMessage()

lowLevelFastqRead

protected boolean lowLevelFastqRead(org.apache.hadoop.io.Text readName,
                                    org.apache.hadoop.io.Text value)
                             throws IOException

Throws:

IOException

next

public boolean next(org.apache.hadoop.io.Text value)
             throws IOException

Reads the next key/value pair from the input for processing.

Throws:

IOException