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

Class PairedEndFastqToTfq

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq

public class PairedEndFastqToTfq
extends Object

This class allow to convert two FASTQ file in one TFQ file.

Since:

2.0

Author:

Laurent Jourdren

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PairedEndFastqToTfq.FastqPairedEndReducer	This class define the reducer required to convert FASTQ files into TFQ file.

Constructor Summary

Constructors

Constructor	Description
PairedEndFastqToTfq()

Method Summary

Modifier and Type	Method	Description
static org.apache.hadoop.mapreduce.Job	convert(org.apache.hadoop.conf.Configuration parentConf, DataFile fastqFile1, DataFile fastqFile2, DataFile outputFile, int reducerTaskCount)	Create the job to convert FASTQ files in a TFQ file.
static org.apache.hadoop.mapreduce.Job	convert(org.apache.hadoop.conf.Configuration parentConf, org.apache.hadoop.fs.Path fastqFile1, org.apache.hadoop.fs.Path fastqFile2, org.apache.hadoop.fs.Path outputFile, int reducerTaskCount)	Create the job to convert FASTQ files in a TFQ file.

Methods inherited from class java.lang.Object

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

Constructor Detail

PairedEndFastqToTfq

public PairedEndFastqToTfq()

Method Detail

convert

public static org.apache.hadoop.mapreduce.Job convert(org.apache.hadoop.conf.Configuration parentConf,
                                                      DataFile fastqFile1,
                                                      DataFile fastqFile2,
                                                      DataFile outputFile,
                                                      int reducerTaskCount)
                                               throws IOException

Create the job to convert FASTQ files in a TFQ file.

Parameters:

parentConf - Hadoop configuration

fastqFile1 - Path of the first FASTQ file

fastqFile2 - Path of the second FASTQ file

outputFile - Path of the output TFQ file

reducerTaskCount - the reducer task count

Returns:

an Hadoop Job

Throws:

IOException - if an error occurs while creating the Job

convert

public static org.apache.hadoop.mapreduce.Job convert(org.apache.hadoop.conf.Configuration parentConf,
                                                      org.apache.hadoop.fs.Path fastqFile1,
                                                      org.apache.hadoop.fs.Path fastqFile2,
                                                      org.apache.hadoop.fs.Path outputFile,
                                                      int reducerTaskCount)
                                               throws IOException

Create the job to convert FASTQ files in a TFQ file.

Parameters:

parentConf - Hadoop configuration

fastqFile1 - Path of the first FASTQ file

fastqFile2 - Path of the second FASTQ file

outputFile - Path of the output TFQ file

reducerTaskCount - the reducer task count

Returns:

an Hadoop Job

Throws:

IOException - if an error occurs while creating the Job