org.seqdoop.hadoop_bam

Class CRAMRecordReader

java.lang.Object

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

org.seqdoop.hadoop_bam.CRAMRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

public class CRAMRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,SAMRecordWritable>

Constructor Summary

Constructors

Constructor and Description
CRAMRecordReader()

Method Summary

Modifier and Type	Method and Description
void	close()
org.apache.hadoop.io.LongWritable	getCurrentKey()
SAMRecordWritable	getCurrentValue()
float	getProgress()
void	initialize(org.apache.hadoop.mapreduce.InputSplit split, org.apache.hadoop.mapreduce.TaskAttemptContext context)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMRecordReader

public CRAMRecordReader()

Method Detail

initialize

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

Specified by:

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

Throws:

IOException

nextKeyValue

public boolean nextKeyValue()

Specified by:

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

getCurrentKey

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

Specified by:

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

getCurrentValue

public SAMRecordWritable getCurrentValue()

Specified by:

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

getProgress

public float getProgress()
                  throws IOException

Specified by:

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

Throws:

IOException

close

public void close()

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.LongWritable,SAMRecordWritable>