com.intel.genomicsdb

Class GenomicsDBRecordReader<VCONTEXT extends htsjdk.tribble.Feature,SOURCE>

java.lang.Object

org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT>

com.intel.genomicsdb.GenomicsDBRecordReader<VCONTEXT,SOURCE>

All Implemented Interfaces:

Closeable, AutoCloseable

@InterfaceAudience.Public
 @InterfaceStability.Stable
public class GenomicsDBRecordReader<VCONTEXT extends htsjdk.tribble.Feature,SOURCE>
extends org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT>

Field Summary

Fields

Modifier and Type	Field and Description
private long	currentKey
private VCONTEXT	currentVariant
private GenomicsDBFeatureReader<VCONTEXT,SOURCE>	featureReader
private htsjdk.tribble.CloseableTribbleIterator<VCONTEXT>	iterator

Constructor Summary

Constructors

Constructor and Description
GenomicsDBRecordReader(GenomicsDBFeatureReader<VCONTEXT,SOURCE> featureReader)

Method Summary

Modifier and Type	Method and Description
void	close()
String	getCurrentKey()
VCONTEXT	getCurrentValue()
float	getProgress()
Boolean	hasNext()
private void	initialize()
void	initialize(org.apache.hadoop.mapreduce.InputSplit inputSplit, org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
boolean	nextKeyValue()

Methods inherited from class java.lang.Object

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

Field Detail

featureReader

private final GenomicsDBFeatureReader<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> featureReader

iterator

private htsjdk.tribble.CloseableTribbleIterator<VCONTEXT extends htsjdk.tribble.Feature> iterator

currentVariant

private VCONTEXT extends htsjdk.tribble.Feature currentVariant

currentKey

private long currentKey

Constructor Detail

GenomicsDBRecordReader

GenomicsDBRecordReader(GenomicsDBFeatureReader<VCONTEXT,SOURCE> featureReader)

Method Detail

initialize

public void initialize(org.apache.hadoop.mapreduce.InputSplit inputSplit,
                       org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
                throws IOException,
                       InterruptedException

Specified by:

initialize in class org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

InterruptedException

initialize

private void initialize()
                 throws IOException

Throws:

IOException

nextKeyValue

public boolean nextKeyValue()
                     throws IOException,
                            InterruptedException

Specified by:

nextKeyValue in class org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

InterruptedException

getCurrentKey

public String getCurrentKey()
                     throws IOException,
                            InterruptedException

Specified by:

getCurrentKey in class org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

InterruptedException

getCurrentValue

public VCONTEXT getCurrentValue()
                         throws IOException,
                                InterruptedException

Specified by:

getCurrentValue in class org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

InterruptedException

getProgress

public float getProgress()
                  throws IOException,
                         InterruptedException

Specified by:

getProgress in class org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

InterruptedException

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<String,VCONTEXT extends htsjdk.tribble.Feature>

Throws:

IOException

hasNext

public Boolean hasNext()