Package fr.ens.biologie.genomique.aozan.aozan3.nanopore

Class BasecallingModelSelector

  • public class BasecallingModelSelector
extends Object
    This class allow to select the model to use with Dorado from parameters like flowcell or kit references.
    Since:
    3.1
    Author:
    Laurent Jourdren

    • Constructor Detail

      • BasecallingModelSelector

        public BasecallingModelSelector​(Path modelsPath)
        Public constructor.
        Parameters:
        modelsPath - path of the Dorado models

    • Method Detail

      • getPoreType

        public static String getPoreType​(String flowcellRef)
        Get the pore type from the flowcell reference
        Parameters:
        flowcellRef - the flow cell reference
        Returns:
        the pore type

      • getChemistryType

        public static String getChemistryType​(String kit)
        Get the chemistry type from the kit reference
        Parameters:
        kit - the kit reference
        Returns:
        the chemistry type

      • withAnalyteType

        public BasecallingModelSelector withAnalyteType​(String analyteType)
        Add a filter based on the analyte type.
        Parameters:
        analyteType - the analyte type
        Returns:
        the object

      • withPoreType

        public BasecallingModelSelector withPoreType​(String poreType)
        Add a filter based on the pore type.
        Parameters:
        poreType - the pore type
        Returns:
        the object

      • withChemistryType

        public BasecallingModelSelector withChemistryType​(String chemistryType)
        Add a filter based on the chemistry type.
        Parameters:
        chemistryType - the chemistry type
        Returns:
        the object

      • withTranslocationSpeed

        public BasecallingModelSelector withTranslocationSpeed​(String translocationSpeed)
        Add a filter based on the translocation speed.
        Parameters:
        translocationSpeed - the translocation speed
        Returns:
        the object

      • withSamplingFrequency

        public BasecallingModelSelector withSamplingFrequency​(String samplingFrequency)
        Add a filter based on the sampling frequency.
        Parameters:
        samplingFrequency - the sampling frequency
        Returns:
        the object

      • withModelType

        public BasecallingModelSelector withModelType​(String modelType)
        Add a filter based on the model type.
        Parameters:
        modelType - the model type
        Returns:
        the object

      • withVersion

        public BasecallingModelSelector withVersion​(String version)
        Add a filter based on the version of the model.
        Parameters:
        version - the requested version of the model
        Returns:
        the object

      • withFlowcellReference

        public BasecallingModelSelector withFlowcellReference​(String flowcell)
        Add a filter based on the flowcell reference.
        Parameters:
        flowcell - the flowcell reference
        Returns:
        the object

      • withKitReference

        public BasecallingModelSelector withKitReference​(String kit)
        Add a filter based on the kit reference.
        Parameters:
        kit - the kit reference
        Returns:
        the object

      • withNoModification

        public BasecallingModelSelector withNoModification()
        Add a filter that reject models that handle modifications.
        Returns:
        the object

      • withModification

        public BasecallingModelSelector withModification​(String modification)
        Add a filter that allow models that handle a modification.
        Parameters:
        modification - required modification
        Returns:
        the object

      • select

        public Path select()
        Select the right model.
        Returns:
        the selected model