Package org.snpsift

Class SnpSiftCmdSplit

java.lang.Object
org.snpsift.SnpSift
org.snpsift.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
  • Field Details

  • Constructor Details

    • SnpSiftCmdSplit

      public SnpSiftCmdSplit()
    • SnpSiftCmdSplit

      public SnpSiftCmdSplit(String[] args)
  • Method Details

    • getFileNames

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

      public 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(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(String msg)
      Show usage message
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift
      Parameters:
      msg -