Package org.snpsift

Class SnpSiftCmdGeneSets

java.lang.Object
org.snpsift.SnpSift
org.snpsift.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

  • Field Details

  • Constructor Details

    • SnpSiftCmdGeneSets

      public SnpSiftCmdGeneSets()

    • SnpSiftCmdGeneSets

      public SnpSiftCmdGeneSets(String[] args)

  • Method Details

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

    • 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()
      Annotate entries
      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)

    • setMsigdb

      public void setMsigdb(String msigdb)

    • usage

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