Package org.snpsift

Class SnpSiftCmdSort

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

public class SnpSiftCmdSort extends SnpSift
Sort VCF file/s by chromosome invalid input: '&' position
Author:
pablocingolani
  • Field Details

  • Constructor Details

    • SnpSiftCmdSort

      public SnpSiftCmdSort()
    • SnpSiftCmdSort

      public SnpSiftCmdSort(String[] args)
  • Method Details

    • loadVcfFiles

      public void loadVcfFiles()
      Load VCF files
    • 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
    • run

      public List<org.snpeff.vcf.VcfEntry> run(boolean createList)
    • usage

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