Package org.snpsift

Class 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 Detail

      • SnpSiftCmdPrivate

        public SnpSiftCmdPrivate()
      • SnpSiftCmdPrivate

        public SnpSiftCmdPrivate​(java.lang.String[] args)
    • Method Detail

      • 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​(java.lang.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 java.util.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​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift