org.seqdoop.hadoop_bam

Class BCFRecordReader

java.lang.Object

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

org.seqdoop.hadoop_bam.BCFRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

public class BCFRecordReader
extends org.apache.hadoop.mapreduce.RecordReader<org.apache.hadoop.io.LongWritable,VariantContextWritable>

See VCFRecordReader for the meaning of the key.

Constructor Summary

Constructors

Constructor and Description
BCFRecordReader()

Method Summary

Modifier and Type	Method and Description
void	close()
org.apache.hadoop.io.LongWritable	getCurrentKey()
VariantContextWritable	getCurrentValue()
float	getProgress() For compressed BCF, unless the end has been reached, this is quite inaccurate.
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

BCFRecordReader

public BCFRecordReader()

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,VariantContextWritable>

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,VariantContextWritable>

Throws:

IOException

getProgress

public float getProgress()

For compressed BCF, unless the end has been reached, this is quite inaccurate.

Specified by:

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

getCurrentKey

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

Specified by:

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

getCurrentValue

public VariantContextWritable getCurrentValue()

Specified by:

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

nextKeyValue

public boolean nextKeyValue()
                     throws IOException

Specified by:

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

Throws:

IOException