Package org.snpsift

Class SnpSiftCmdPrivate

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdPrivate
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdPrivate extends SnpSift
Annotate if a variant is 'private'. I.e. only represented within a family (or group)
Author:
pcingola

  • Constructor Details

    • SnpSiftCmdPrivate

      public SnpSiftCmdPrivate()

    • SnpSiftCmdPrivate

      public SnpSiftCmdPrivate(String[] args)

  • Method Details

    • annotate

      public boolean annotate(org.snpeff.vcf.VcfEntry ve)
      Parse a single VCF entry
      Specified by:
      annotate in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotate in class SnpSift

    • annotateInit

      public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
      Specified by:
      annotateInit in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotateInit 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 annotations
      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. Create a list of VcfEntries if 'createList' is true (use for test cases)

    • usage

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