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

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • 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
      threads - thread count to use
      storage - the genome index storage
      temporaryDirectory - temporary directory for the indexer
      logger - the logger

  • Method Details

    • 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