Package org.snpsift

Class SnpSiftCmdSplit

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

    public class SnpSiftCmdSplit
    extends SnpSift
    Split a large VCF file by chromosome or bby number of lines
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdSplit

        public SnpSiftCmdSplit()
      • SnpSiftCmdSplit

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

      • getFileNames

        public java.util.ArrayList<java.lang.String> getFileNames()
        Names of files created when splitting
        Returns:
      • join

        public java.lang.String join​(boolean createString)
        Join files
        Parameters:
        createString - : Create a string used for test cases)
        Returns:
        A string with the resulting file if createString is true. An empty string otherwise.
      • 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
      • 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 -