org.seqdoop.hadoop_bam

Class SAMRecordReader

java.lang.Object

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

org.seqdoop.hadoop_bam.SAMRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

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

See BAMRecordReader for the meaning of the key.

Constructor Summary

Constructors

Constructor and Description
SAMRecordReader()

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 spl, org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMRecordReader

public SAMRecordReader()

Method Detail

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit spl,
                       org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                throws IOException

Specified by:

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

Throws:

IOException

close

public void close()
           throws IOException

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>

Throws:

IOException

getProgress

public float getProgress()
                  throws IOException

Specified by:

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

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,SAMRecordWritable>

getCurrentValue

public SAMRecordWritable getCurrentValue()

Specified by:

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

nextKeyValue

public boolean nextKeyValue()

Specified by:

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