Package org.snpsift

Class 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 Detail

      • 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 java.lang.String chrPrev
      • prependInfoFieldName

        protected java.lang.String prependInfoFieldName
      • existsInfoField

        protected java.lang.String existsInfoField
      • infoFields

        protected java.util.ArrayList<java.lang.String> infoFields
      • vcfFile

        protected org.snpeff.fileIterator.VcfFileIterator vcfFile
    • Constructor Detail

      • SnpSiftCmdAnnotate

        public SnpSiftCmdAnnotate()
      • SnpSiftCmdAnnotate

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

      • 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 java.util.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​(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 each entry of a VCF file
        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)
        Run annotations
        Parameters:
        createList - : If true, return a list with all annotated entries (used for test cases & debugging)
      • setAnnotateEmpty

        public void setAnnotateEmpty​(boolean annotateEmpty)
      • 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