Package org.snpsift

Class SnpSiftCmdGeneSets

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdGeneSets
    extends SnpSift
    Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdGeneSets

        public SnpSiftCmdGeneSets()
      • SnpSiftCmdGeneSets

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

      • annotate

        public boolean annotate​(org.snpeff.vcf.VcfEntry vcfEntry)
        Annotate one 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
      • headers

        protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
        Description copied from class: SnpSift
        Headers to add
        Overrides:
        headers in class SnpSift
      • parseArgs

        public void parseArgs​(java.lang.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()
        Annotate entries
        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)
      • setMsigdb

        public void setMsigdb​(java.lang.String msigdb)
      • 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