Package ngs

Interface Pileup

    • Method Detail

      • getReferenceSpec

        java.lang.String getReferenceSpec()
                                   throws ErrorMsg
        getReferenceSpec
        Returns:
        name of the Reference
        Throws:
        ErrorMsg - upon an error accessing data
      • getReferencePosition

        long getReferencePosition()
                           throws ErrorMsg
        getReferencePosition
        Returns:
        current position on the Reference
        Throws:
        ErrorMsg - upon an error accessing data
      • getReferenceBase

        char getReferenceBase()
                       throws ErrorMsg
        Returns:
        base at current Reference position
        Throws:
        ErrorMsg - upon an error accessing data
      • getPileupDepth

        int getPileupDepth()
                    throws ErrorMsg
        getPileupDepth
        Returns:
        the coverage depth at the current reference position
        Throws:
        ErrorMsg - upon an error accessing data