Package org.snpsift

Class SnpSiftCmdAnnotate

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdAnnotate
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdAnnotate extends SnpSift
Annotate a VCF file with ID from another VCF file (database)
Author:
pcingola

  • Field Details

    • SHOW

      public static final int SHOW
      See Also:

    • annotateEmpty

      protected boolean annotateEmpty

    • useId

      protected boolean useId

    • useInfoField

      protected boolean useInfoField

    • useRefAlt

      protected boolean useRefAlt

    • method

      protected org.snpsift.SnpSiftCmdAnnotate.AnnotationMethod method

    • countBadRef

      protected int countBadRef

    • maxBlockSize

      protected int maxBlockSize

    • chrPrev

      protected String chrPrev

    • prependInfoFieldName

      protected String prependInfoFieldName

    • existsInfoField

      protected String existsInfoField

    • infoFields

      protected ArrayList<String> infoFields

    • vcfFile

      protected org.snpeff.fileIterator.VcfFileIterator vcfFile

    • annotateDb

      protected AnnotateVcfDb annotateDb

  • Constructor Details

    • SnpSiftCmdAnnotate

      public SnpSiftCmdAnnotate()

    • SnpSiftCmdAnnotate

      public SnpSiftCmdAnnotate(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

    • 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

    • headers

      protected List<org.snpeff.vcf.VcfHeaderEntry> headers()
      Build 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

    • 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)

    • setAnnotateEmpty

      public void setAnnotateEmpty(boolean annotateEmpty)

    • usage

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