Class CountSplicedReadsModule

  • All Implemented Interfaces:
    Module

    public class CountSplicedReadsModule
    extends AbstractModule
    This step computes how many spliced alignments there are in a SAM file. This QC step computes the number of spliced alignments in a SAM file, as well as the total number of mapped reads.
    Author:
    Celine Hernandez - CSB lab - ENS - Paris
    • Constructor Detail

      • CountSplicedReadsModule

        public CountSplicedReadsModule()
    • Method Detail

      • getName

        public String getName()
        Name of the Step.
        Returns:
        the name of the module
      • getVersion

        public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
        Version.
        Returns:
        a Version object with the version of the Module
      • execute

        public TaskResult execute​(TaskContext context,
                                  TaskStatus status)
        Install all the files necessary in the tmp folder, then run idr.
        Parameters:
        context - Execution context
        status - of the task