Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdEff

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdEff
All Implemented Interfaces:
CommandLine, VcfAnnotator
public class SnpEffCmdEff extends SnpEff implements VcfAnnotator
Command line program: Predict variant effects
Author:
Pablo Cingolani

  • Field Details

  • Constructor Details

    • SnpEffCmdEff

      public SnpEffCmdEff()

  • Method Details

    • addHeaders

      public boolean addHeaders(VcfFileIterator vcfFile)
      Description copied from interface: VcfAnnotator
      Add annotation headers to VCF file
      Specified by:
      addHeaders in interface VcfAnnotator
      Returns:
      true if OK, false on error

    • annotate

      public boolean annotate(String inputFile, String outputFile)
      Annotate: Calculate the effect of variants and show results

    • annotate

      public boolean annotate(VcfEntry vcfEntry)
      Annotate a VCF entry
      Specified by:
      annotate in interface VcfAnnotator
      Returns:
      true if the entry was annotated

    • annotateFinish

      public boolean annotateFinish(VcfFileIterator vcfFile)
      Finish annotations and create reports
      Specified by:
      annotateFinish in interface VcfAnnotator
      Returns:
      true if OK, false on error

    • annotateInit

      protected void annotateInit(String outputFile)
      Calculate the effect of variants and show results

    • annotateInit

      public boolean annotateInit(VcfFileIterator vcfFile)
      Description copied from interface: VcfAnnotator
      Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.
      Specified by:
      annotateInit in interface VcfAnnotator
      Returns:
      true if OK, false on error

    • getChangeEffectResutStats

      public VariantEffectStats getChangeEffectResutStats()

    • getTotalErrs

      public int getTotalErrs()

    • getvariantStats

      public VariantStats getvariantStats()

    • parseArgs

      public void parseArgs(String[] args)
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine
      Overrides:
      parseArgs in class SnpEff

    • reportValues

      public HashMap<String,String> reportValues()
      Description copied from class: SnpEff
      Additional values to be reported
      Overrides:
      reportValues in class SnpEff

    • run

      public boolean run()
      Run according to command line options
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • run

      public List<VcfEntry> run(boolean createList)
      Run according to command line options

    • setFormatVersion

      public void setFormatVersion(EffFormatVersion formatVersion)

    • usage

      public void usage(String message)
      Show 'usage;' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine
      Overrides:
      usage in class SnpEff
      Parameters:
      message -