Package fr.ens.biologie.genomique.eoulsan.data.storages

Class DataFileGenomeMapperIndexer

java.lang.Object

fr.ens.biologie.genomique.kenetre.storage.FileGenomeMapperIndexer

fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer

public class DataFileGenomeMapperIndexer
extends fr.ens.biologie.genomique.kenetre.storage.FileGenomeMapperIndexer

This class define a genome mapper indexer.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
DataFileGenomeMapperIndexer(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance, String additionalArguments, Map<String,String> additionalDescription, int threads, fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage storage, File temporaryDirectory, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	createIndex(DataFile genomeDataFile, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription, DataFile mapperIndexDataFile)	Create an archived genome index.

Methods inherited from class fr.ens.biologie.genomique.kenetre.storage.FileGenomeMapperIndexer

createIndex, createIndex

Methods inherited from class java.lang.Object

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

Constructor Detail

DataFileGenomeMapperIndexer

public DataFileGenomeMapperIndexer(fr.ens.biologie.genomique.kenetre.bio.readmapper.MapperInstance mapperInstance,
                                   String additionalArguments,
                                   Map<String,String> additionalDescription,
                                   int threads,
                                   fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage storage,
                                   File temporaryDirectory,
                                   fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Public constructor.

Parameters:

mapperInstance - Mapper to use for the index generator

additionalArguments - additional indexer arguments

additionalDescription - additional indexer arguments description

storage - the genome index storage

temporaryDirectory - temporary directory for the indexer

logger - the logger

Method Detail

createIndex

public void createIndex(DataFile genomeDataFile,
                        fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDescription,
                        DataFile mapperIndexDataFile)
                 throws IOException

Create an archived genome index.

Parameters:

genomeDataFile - genome to index

genomeDescription - description of the genome

mapperIndexDataFile - output genome index archive

Throws:

IOException - if an error occurs while creating the genome