Package org.snpsift

Class SnpSiftCmdGwasCatalog

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdGwasCatalog
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdGwasCatalog extends SnpSift
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
Author:
pablocingolani

  • Field Details

  • Constructor Details

    • SnpSiftCmdGwasCatalog

      public SnpSiftCmdGwasCatalog()

    • SnpSiftCmdGwasCatalog

      public SnpSiftCmdGwasCatalog(String[] args)

  • Method Details

    • annotate

      public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
      Specified by:
      annotate in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotate in class SnpSift

    • annotateFinish

      public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
      Specified by:
      annotateFinish in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotateFinish 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

    • init

      public void init()
      Initialize default values
      Overrides:
      init 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

    • readDb

      public void readDb()
      Read database

    • 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 saveResults)

    • usage

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