Package org.snpsift

Class SnpSiftCmdIntervalsIndex

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

    public class SnpSiftCmdIntervalsIndex
    extends SnpSift
    Filter variants that hit intervals Use an indexed VCF file. WARNIGN: File must be uncompressed
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdIntervalsIndex

        public SnpSiftCmdIntervalsIndex()
      • SnpSiftCmdIntervalsIndex

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

      • init

        public void init()
        Description copied from class: SnpSift
        Initialize default values
        Overrides:
        init in class SnpSift
      • loadIntervals

        public void loadIntervals()
        Load all BED files
        Parameters:
        bedFileNames -
      • parseArgs

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

        public boolean run()
        Load a file compare calls
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
        Parameters:
        fileName -
      • setInOffset

        public void setInOffset​(int inOffset)
      • 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 -