Package org.snpsift

Class SnpSiftCmdIntersect

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdIntersect
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdIntersect extends SnpSift
Intersect intervals
Author:
pcingola
  • Constructor Details

    • SnpSiftCmdIntersect

      public SnpSiftCmdIntersect()
    • SnpSiftCmdIntersect

      public SnpSiftCmdIntersect(String[] args)
  • Method Details

    • parseArgs

      public void parseArgs(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 annotations
      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 -