Class AbstractReadsMapperModule

    • Constructor Detail

      • AbstractReadsMapperModule

        public AbstractReadsMapperModule()
    • Method Detail

      • getMapperName

        protected String getMapperName()
        Get the name of the mapper to use.
        Returns:
        Returns the mapperName
      • getMapperVersion

        protected String getMapperVersion()
        Get the version of the mapper to use.
        Returns:
        the version of the mapper to use
      • getMapperFlavor

        protected String getMapperFlavor()
        Get the flavor of the mapper to use.
        Returns:
        the flavor of the mapper to use
      • isUseBundledBinaries

        protected boolean isUseBundledBinaries()
        Test if the bundled binaries must be used to perform the step.
        Returns:
        true if the bundled binaries must be used to perform the step
      • getMapperDockerImage

        protected String getMapperDockerImage()
        Get the mapper Docker image to use.
        Returns:
        the mapper Docker image to use
      • getMapperArguments

        protected String getMapperArguments()
        Get the arguments of the mapper to use.
        Returns:
        Returns the mapperArguments
      • getMapperLocalThreads

        protected int getMapperLocalThreads()
        Get the number of threads to use in local mode.
        Returns:
        Returns the mapperThreads
      • getMapperHadoopThreads

        protected int getMapperHadoopThreads()
        Get the number of threads to use in local mode.
        Returns:
        Returns the mapperThreads
      • getMapperHadoopMemoryRequired

        protected int getMapperHadoopMemoryRequired()
        Get the amount in MB of memory required to execute the mapper. This value is required by Hadoop scheduler and if the mapper require more memory than declared the mapper process will be killed.
        Returns:
        the amount of memory required by the mapper in MB
      • getMapper

        protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper getMapper()
        Get the mapper object.
        Returns:
        the mapper object
      • getReducerTaskCount

        protected int getReducerTaskCount()
        Get the reducer task count.
        Returns:
        the reducer task count
      • getName

        public String getName()
        Description copied from interface: Module
        Get the name of the module.
        Returns:
        the name of the module
      • getVersion

        public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
        Description copied from interface: Module
        Get version of the Module.
        Returns:
        a Version object with the version of the Module