Package org.snpsift

Class SnpSiftCmdSort

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

    public class SnpSiftCmdSort
    extends SnpSift
    Sort VCF file/s by chromosome & position
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdSort

        public SnpSiftCmdSort()
      • SnpSiftCmdSort

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

      • loadVcfFiles

        public void loadVcfFiles()
        Load VCF files
      • 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
        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)
      • 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