org.seqdoop.hadoop_bam

Class VCFRecordReader

java.lang.Object

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

org.seqdoop.hadoop_bam.VCFRecordReader

All Implemented Interfaces:

Closeable, AutoCloseable

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

The key is the bitwise OR of the chromosome index in the upper 32 bits and the 0-based leftmost coordinate in the lower. The chromosome index is based on the ordering of the contig lines in the VCF header. If a chromosome name that cannot be found in the contig lines is used, that name is instead hashed to form the upper part of the key.

Constructor Summary

Constructors

Constructor and Description
VCFRecordReader()

Method Summary

Modifier and Type	Method and Description
void	close()
org.apache.hadoop.io.LongWritable	getCurrentKey()
VariantContextWritable	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

VCFRecordReader

public VCFRecordReader()

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()
                  throws IOException

Specified by:

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

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,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