Package org.snpsift

Class SnpSiftCmdPhastCons

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

    public class SnpSiftCmdPhastCons
    extends SnpSift
    Annotate using PhastCons score files
    Author:
    pcingola
    • Constructor Detail

      • SnpSiftCmdPhastCons

        public SnpSiftCmdPhastCons()
      • SnpSiftCmdPhastCons

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

      • init

        public void init()
        Description copied from class: SnpSift
        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()
        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)
        Run annotations
        Parameters:
        createList - : If true, create a list of VcfEntries (used for test cases)
        Returns:
      • 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 -