Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli

Class CLIMergingAnySAMOutputFormat<K>

java.lang.Object

org.apache.hadoop.mapreduce.OutputFormat<K,V>

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat<K>

public class CLIMergingAnySAMOutputFormat<K>
extends org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.Counter

Field Summary

Fields inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

BASE_OUTPUT_NAME, COMPRESS, COMPRESS_CODEC, COMPRESS_TYPE, OUTDIR, PART

Constructor Summary

Constructors

Constructor	Description
CLIMergingAnySAMOutputFormat()

Method Summary

Modifier and Type	Method	Description
void	checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)
org.apache.hadoop.fs.Path	getDefaultWorkFile(org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String ext)
org.apache.hadoop.mapreduce.RecordWriter<K,org.seqdoop.hadoop_bam.SAMRecordWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext context)

Methods inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

getCompressOutput, getOutputCommitter, getOutputCompressorClass, getOutputName, getOutputPath, getPathForWorkFile, getUniqueFile, getWorkOutputPath, setCompressOutput, setOutputCompressorClass, setOutputName, setOutputPath

Methods inherited from class java.lang.Object

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

Constructor Detail

CLIMergingAnySAMOutputFormat

public CLIMergingAnySAMOutputFormat()

Method Detail

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<K,org.seqdoop.hadoop_bam.SAMRecordWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext context)
                                                                                                           throws IOException

Specified by:

getRecordWriter in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>

Throws:

IOException

getDefaultWorkFile

public org.apache.hadoop.fs.Path getDefaultWorkFile(org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
                                                    String ext)
                                             throws IOException

Overrides:

getDefaultWorkFile in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>

Throws:

IOException

checkOutputSpecs

public void checkOutputSpecs(org.apache.hadoop.mapreduce.JobContext job)

Overrides:

checkOutputSpecs in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,org.seqdoop.hadoop_bam.SAMRecordWritable>