Package org.snpsift

Class SnpSiftCmdIntervals

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdIntervals
    extends SnpSift
    Filter variants that hit intervals
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdIntervals

        public SnpSiftCmdIntervals()
      • SnpSiftCmdIntervals

        public SnpSiftCmdIntervals​(java.lang.String[] args)
    • Method Detail

      • init

        public void init()
        Initialize default values
        Overrides:
        init in class SnpSift
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Description copied from class: SnpSift
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • run

        public boolean run()
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • run

        public java.util.List<org.snpeff.vcf.VcfEntry> run​(boolean createList)
        Load a file compare calls
        Parameters:
        fileName -
      • usage

        public void usage​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift
        Parameters:
        msg -