Class SnpSiftCmdPhastCons

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdPhastCons
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdPhastCons extends SnpSift
Annotate using PhastCons score files
Author:
pcingola

  • Field Details

  • Constructor Details

    • SnpSiftCmdPhastCons

      public SnpSiftCmdPhastCons()

    • SnpSiftCmdPhastCons

      public SnpSiftCmdPhastCons(String[] args)

  • Method Details

    • init

      public void init()
      Description copied from class: SnpSift
      Initialize default values
      Overrides:
      init in class SnpSift

    • 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
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift

    • run

      public List<org.snpeff.vcf.VcfEntry> run(boolean createList)
      Run annotations
      Parameters:
      createList - : If true, create a list of VcfEntries (used for test cases)
      Returns:

    • 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 -