Package org.snpsift

Class SnpSiftCmdAnnotateDf

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdAnnotateDf
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdAnnotateDf extends SnpSift
Annotate a VCF file from another VCF file (database) by creating "DataFrames" for each chromosome. The database file is loaded into memory.
Author:
pcingola

  • Constructor Details

    • SnpSiftCmdAnnotateDf

      public SnpSiftCmdAnnotateDf()

    • SnpSiftCmdAnnotateDf

      public SnpSiftCmdAnnotateDf(String[] args)

  • Method Details

    • add

      public void add(String dbFileName)
      Add a database file

    • 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()

    • annotateInit

      public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
      Initialize database for annotation process
      Specified by:
      annotateInit in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotateInit in class SnpSift

    • create

      public void create()
      Create all databases

    • headers

      protected List<org.snpeff.vcf.VcfHeaderEntry> headers()
      Build headers to add
      Overrides:
      headers in class SnpSift

    • init

      public void init()
      Initialize
      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

    • run

      public boolean run()
      Annotate each entry of a VCF file
      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
      Parameters:
      createList - : If true, return a list with all annotated entries (used for test cases invalid input: '&' debugging)

    • usage

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