Package fr.ens.biologie.genomique.aozan.fastqscreen

Class FastqScreen

java.lang.Object

fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreen

public class FastqScreen
extends Object

This class execute fastqscreen pair-end mode or single-end.

Since:

1.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
FastqScreen(CollectorConfiguration conf)	Public constructor of fastqscreen.

Method Summary

Modifier and Type	Method	Description
FastqScreenResult	execute(File fastqRead1, File fastqRead2, String sampleDescription, List<String> genomes, String sampleGenome, boolean isPairedMode)	Mode single-end : execute fastqscreen.
FastqScreenResult	execute(File fastqRead, String sampleDescription, List<String> genomes, String genomeSample, boolean paired)	Mode pair-end : execute fastqscreen.
FastqScreenGenomes	getFastqScreenGenomes()

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqScreen

public FastqScreen(CollectorConfiguration conf)

Public constructor of fastqscreen. Initialization of settings of Eoulsan necessary for use of mapper index.

Parameters:

conf - Collector configuration

Method Detail

getFastqScreenGenomes

public FastqScreenGenomes getFastqScreenGenomes()
                                         throws AozanException

Throws:

AozanException

execute

public FastqScreenResult execute(File fastqRead,
                                 String sampleDescription,
                                 List<String> genomes,
                                 String genomeSample,
                                 boolean paired)
                          throws AozanException

Mode pair-end : execute fastqscreen.

Parameters:

fastqRead - fastq file input for mapper

sampleDescription - sample description

genomes - list or reference genome, used by mapper

genomeSample - genome reference corresponding to sample

Returns:

FastqScreenResult object contains results for each reference genome

Throws:

AozanException

execute

public FastqScreenResult execute(File fastqRead1,
                                 File fastqRead2,
                                 String sampleDescription,
                                 List<String> genomes,
                                 String sampleGenome,
                                 boolean isPairedMode)
                          throws AozanException

Mode single-end : execute fastqscreen.

Parameters:

fastqRead1 - fastq read1 file input for mapper

fastqRead2 - fastq read2 file input for mapper

sampleDescription - sample description

genomes - list or reference genome, used by mapper

sampleGenome - genome reference corresponding to sample

isPairedMode - true if a pair-end run and option paired mode equals true else false

Throws:

AozanException