org.seqdoop.hadoop_bam

Class FastaInputFormat.FastaRecordReader

java.lang.Object

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

org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

Enclosing class:

FastaInputFormat

public static class FastaInputFormat.FastaRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.Text,ReferenceFragment>

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_LINE_LENGTH

Constructor Summary

Constructors

Constructor and Description
FastaRecordReader(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.
ReferenceFragment	createValue() Create an object of the appropriate type to be used as a value.
org.apache.hadoop.io.Text	getCurrentKey() Added to use mapreduce API.
ReferenceFragment	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.
String	makePositionMessage()
String	makePositionMessage(long pos)
boolean	next(org.apache.hadoop.io.Text key, ReferenceFragment value) Reads the next key/value pair from the input for processing.
boolean	nextKeyValue() Added to use mapreduce API.
protected void	setConf(org.apache.hadoop.conf.Configuration conf)

Methods inherited from class java.lang.Object

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

Field Detail

MAX_LINE_LENGTH

public static final int MAX_LINE_LENGTH

See Also:

Constant Field Values

Constructor Detail

FastaRecordReader

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

Throws:

IOException

Method Detail

setConf

protected void setConf(org.apache.hadoop.conf.Configuration conf)

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<org.apache.hadoop.io.Text,ReferenceFragment>

Throws:

IOException

InterruptedException

getCurrentKey

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

Added to use mapreduce API.

Specified by:

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

getCurrentValue

public ReferenceFragment getCurrentValue()

Added to use mapreduce API.

Specified by:

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

nextKeyValue

public boolean nextKeyValue()
                     throws IOException,
                            InterruptedException

Added to use mapreduce API.

Specified by:

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

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<org.apache.hadoop.io.Text,ReferenceFragment>

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 ReferenceFragment 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<org.apache.hadoop.io.Text,ReferenceFragment>

makePositionMessage

public String makePositionMessage(long pos)

makePositionMessage

public String makePositionMessage()

next

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

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

Throws:

IOException