Package org.snpsift

Class SnpSiftCmdExtractFields

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

    public class SnpSiftCmdExtractFields
    extends SnpSift
    Extract fields from VCF file to a TXT (tab separated) format
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdExtractFields

        public SnpSiftCmdExtractFields()
      • SnpSiftCmdExtractFields

        public SnpSiftCmdExtractFields​(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)
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • run

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

        public java.util.List<java.lang.String> run​(boolean createList)
      • 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 -