net.maizegenetics.pangenome.hapCalling

Class CreateHapIdMapsPlugin

net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin

public class CreateHapIdMapsPlugin

Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG. This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network. By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.

Constructor Detail

CreateHapIdMapsPlugin

public CreateHapIdMapsPlugin(@Nullable
                             java.awt.Frame parentFrame,
                             boolean isInteractive)

Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG. This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network. By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.

CreateHapIdMapsPlugin

public CreateHapIdMapsPlugin()

Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG. This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network. By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

createAndWriteHapIdMaps

public void createAndWriteHapIdMaps(@NotNull
                                    java.util.Map<java.lang.Integer,? extends net.maizegenetics.pangenome.api.ReferenceRange> hapIdToRefRangeMap,
                                    @NotNull
                                    java.util.Map<java.lang.Integer,java.lang.Integer> hapIdToLengthMap,
                                    @NotNull
                                    java.util.Map<java.lang.Integer,? extends java.util.Map<java.lang.Integer,java.lang.Integer>> refRangeToHapIdMap,
                                    int haplotypeListId,
                                    @NotNull
                                    java.util.Map<java.lang.Integer,? extends java.util.List<java.lang.String>> hapIdToTaxaListMap,
                                    @NotNull
                                    java.lang.String outputFileName)

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

outputMapFile

@NotNull
public java.lang.String outputMapFile()

Output File Name. JSON file will be written

Returns:

Output File Name

outputMapFile

@NotNull
public CreateHapIdMapsPlugin outputMapFile(@NotNull
                                                    java.lang.String value)

Set Output File Name. Output File Name. JSON file will be written

Parameters:

value - Output File Name

Returns:

this plugin

outputTaxaNames

public boolean outputTaxaNames()

Output the Hapid -> TaxaName list Map.

Returns:

Output Taxa Names

outputTaxaNames

@NotNull
public CreateHapIdMapsPlugin outputTaxaNames(boolean value)

Set Output Taxa Names. Output the Hapid -> TaxaName list Map.

Parameters:

value - Output Taxa Names

Returns:

this plugin