public class GenomicsDBInputFormat<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> extends org.apache.hadoop.mapreduce.InputFormat<String,VCONTEXT> implements org.apache.hadoop.conf.Configurable
| Modifier and Type | Field and Description |
|---|---|
private org.apache.hadoop.conf.Configuration |
configuration |
private GenomicsDBConfiguration |
genomicsDBConfiguration |
(package private) org.apache.log4j.Logger |
logger |
| Constructor and Description |
|---|
GenomicsDBInputFormat()
default constructor
|
GenomicsDBInputFormat(GenomicsDBConfiguration conf) |
| 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
|
private GenomicsDBConfiguration genomicsDBConfiguration
private org.apache.hadoop.conf.Configuration configuration
org.apache.log4j.Logger logger
public GenomicsDBInputFormat()
public GenomicsDBInputFormat(GenomicsDBConfiguration conf)
public List<org.apache.hadoop.mapreduce.InputSplit> getSplits(org.apache.hadoop.mapreduce.JobContext jobContext) throws FileNotFoundException
getSplits in class org.apache.hadoop.mapreduce.InputFormat<String,VCONTEXT extends htsjdk.tribble.Feature>jobContext - Hadoop Job context passed from newAPIHadoopRDD
defined in SparkContextFileNotFoundException - Thrown if creaing configuration object failspublic org.apache.hadoop.mapreduce.RecordReader<String,VCONTEXT> createRecordReader(org.apache.hadoop.mapreduce.InputSplit inputSplit, org.apache.hadoop.mapreduce.TaskAttemptContext taskAttemptContext) throws IOException, InterruptedException
createRecordReader in class org.apache.hadoop.mapreduce.InputFormat<String,VCONTEXT extends htsjdk.tribble.Feature>IOExceptionInterruptedExceptionpublic GenomicsDBInputFormat<VCONTEXT,SOURCE> setLoaderJsonFile(String jsonFile)
jsonFile - Full qualified path of the loader JSON filepublic GenomicsDBInputFormat<VCONTEXT,SOURCE> setQueryJsonFile(String jsonFile)
jsonFile - Full qualified path of the query JSON filepublic GenomicsDBInputFormat<VCONTEXT,SOURCE> setHostFile(String hostFile) throws FileNotFoundException
hostFile - Full qualified path of the hosts fileFileNotFoundException - thrown if the hosts file is not foundpublic void setConf(org.apache.hadoop.conf.Configuration configuration)
setConf in interface org.apache.hadoop.conf.Configurablepublic org.apache.hadoop.conf.Configuration getConf()
getConf in interface org.apache.hadoop.conf.ConfigurableCopyright © 2017. All rights reserved.