com.intel.genomicsdb

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

java.lang.Object

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

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

All Implemented Interfaces:

org.apache.hadoop.conf.Configurable

public class GenomicsDBInputFormat<VCONTEXT extends htsjdk.tribble.Feature,SOURCE>
extends org.apache.hadoop.mapreduce.InputFormat<String,VCONTEXT>
implements org.apache.hadoop.conf.Configurable

Field Summary

Fields

Modifier and Type	Field and Description
private org.apache.hadoop.conf.Configuration	configuration
private GenomicsDBConfiguration	genomicsDBConfiguration
(package private) org.apache.log4j.Logger	logger

Constructor Summary

Constructors

Constructor and Description
GenomicsDBInputFormat() default constructor
GenomicsDBInputFormat(GenomicsDBConfiguration conf)

Method Summary

Modifier and Type	Method and Description
org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT>	createRecordReader(org.apache.hadoop.mapreduce.InputSplit inputSplit, org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
org.apache.hadoop.conf.Configuration	getConf()
List<org.apache.hadoop.mapreduce.InputSplit>	getSplits(org.apache.hadoop.mapreduce.JobContext jobContext) When this function is called, it is already assumed that configuration object is set
void	setConf(org.apache.hadoop.conf.Configuration configuration)
GenomicsDBInputFormat<VCONTEXT,SOURCE>	setHostFile(String hostFile) Set the host file path
GenomicsDBInputFormat<VCONTEXT,SOURCE>	setLoaderJsonFile(String jsonFile) Set the loader JSON file path
GenomicsDBInputFormat<VCONTEXT,SOURCE>	setQueryJsonFile(String jsonFile) Set the query JSON file path

Methods inherited from class java.lang.Object

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

Field Detail

genomicsDBConfiguration

private GenomicsDBConfiguration genomicsDBConfiguration

configuration

private org.apache.hadoop.conf.Configuration configuration

logger

org.apache.log4j.Logger logger

Constructor Detail

GenomicsDBInputFormat

public GenomicsDBInputFormat()

default constructor

GenomicsDBInputFormat

public GenomicsDBInputFormat(GenomicsDBConfiguration conf)

Method Detail

getSplits

public List<org.apache.hadoop.mapreduce.InputSplit> getSplits(org.apache.hadoop.mapreduce.JobContext jobContext)
                                                       throws FileNotFoundException

When this function is called, it is already assumed that configuration object is set

Specified by:

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

Parameters:

jobContext - Hadoop Job context passed from newAPIHadoopRDD defined in SparkContext

Returns:

Returns a list of input splits

Throws:

FileNotFoundException - Thrown if creaing configuration object fails

createRecordReader

public org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT> createRecordReader(org.apache.hadoop.mapreduce.InputSplit inputSplit,
                                                                                    org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext)
                                                                             throws IOException,
                                                                                    InterruptedException

Specified by:

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

Throws:

IOException

InterruptedException

setLoaderJsonFile

public GenomicsDBInputFormat<VCONTEXT,SOURCE> setLoaderJsonFile(String jsonFile)

Set the loader JSON file path

Parameters:

jsonFile - Full qualified path of the loader JSON file

Returns:

Returns the same object for forward function calls

setQueryJsonFile

public GenomicsDBInputFormat<VCONTEXT,SOURCE> setQueryJsonFile(String jsonFile)

Set the query JSON file path

Parameters:

jsonFile - Full qualified path of the query JSON file

Returns:

Returns the same object for forward function calls

setHostFile

public GenomicsDBInputFormat<VCONTEXT,SOURCE> setHostFile(String hostFile)
                                                   throws FileNotFoundException

Set the host file path

Parameters:

hostFile - Full qualified path of the hosts file

Returns:

Returns the same object for forward function calls

Throws:

FileNotFoundException - thrown if the hosts file is not found

setConf

public void setConf(org.apache.hadoop.conf.Configuration configuration)

Specified by:

setConf in interface org.apache.hadoop.conf.Configurable

getConf

public org.apache.hadoop.conf.Configuration getConf()

Specified by:

getConf in interface org.apache.hadoop.conf.Configurable