net.maizegenetics.pangenome.pipeline

Class ImputePipelinePlugin

net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin

public class ImputePipelinePlugin

Constructor Detail

ImputePipelinePlugin

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

ImputePipelinePlugin

public ImputePipelinePlugin()

Method Detail

postProcessParameters

protected void postProcessParameters()

processData

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

getToolTipText

@NotNull
public java.lang.String getToolTipText()

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

imputeTarget

@NotNull
public net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin.IMPUTE_TASK imputeTarget()

Specifies the target or desired endpoint when running the plugin. For any given endpoint, the plugin will check that all required previous step have been completed and run those as needed.

Returns:

Impute Target

imputeTarget

@NotNull
public ImputePipelinePlugin imputeTarget(@NotNull
                                                  net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin.IMPUTE_TASK value)

Set Impute Target. Specifies the target or desired endpoint when running the plugin. For any given endpoint, the plugin will check that all required previous step have been completed and run those as needed.

Parameters:

value - Impute Target

Returns:

this plugin

inputType

@NotNull
public net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin.INPUT_TYPE inputType()

The type of data to be used for imputation

Returns:

Input Type

inputType

@NotNull
public ImputePipelinePlugin inputType(@NotNull
                                               net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin.INPUT_TYPE value)

Set Input Type. The type of data to be used for imputation

Parameters:

value - Input Type

Returns:

this plugin

configFile

@Nullable
public java.lang.String configFile()

The config file name.

Returns:

Config File

configFile

@NotNull
public ImputePipelinePlugin configFile(@NotNull
                                                java.lang.String value)

Set Config File. The config file name.

Parameters:

value - Config File

Returns:

this plugin

pangenomeHaplotypeMethod

@NotNull
public java.lang.String pangenomeHaplotypeMethod()

The haplotype method used to create the pangenome.fa and pangenome.mmi.

Returns:

Pangenome Haplotype Method

pangenomeHaplotypeMethod

@NotNull
public ImputePipelinePlugin pangenomeHaplotypeMethod(@NotNull
                                                              java.lang.String value)

Set Pangenome Haplotype Method. The haplotype method used to create the pangenome.fa and pangenome.mmi.

Parameters:

value - Pangenome Haplotype Method

Returns:

this plugin

pathHaplotypeMethod

@NotNull
public java.lang.String pathHaplotypeMethod()

The haplotype method used to impute a path. The same method will be used to create the PHG used for read mapping.

Returns:

Path Haplotype Method

pathHaplotypeMethod

@NotNull
public ImputePipelinePlugin pathHaplotypeMethod(@NotNull
                                                         java.lang.String value)

Set Path Haplotype Method. The haplotype method used to impute a path. The same method will be used to create the PHG used for read mapping.

Parameters:

value - Path Haplotype Method

Returns:

this plugin

pangenomeDir

@NotNull
public java.lang.String pangenomeDir()

The directory of the pangenome file and index.

Returns:

Pangenome Dir

pangenomeDir

@NotNull
public ImputePipelinePlugin pangenomeDir(@NotNull
                                                  java.lang.String value)

Set Pangenome Dir. The directory of the pangenome file and index.

Parameters:

value - Pangenome Dir

Returns:

this plugin

pangenomeIndexName

@Nullable
public java.lang.String pangenomeIndexName()

WARNING: By default the plugin will construct pangenome file and index names from the pangenomeHaplotypeMethod. Only use this parameter to over-ride that name with a different one. Be sure the pangenomeHaplotypeMethod matches the index.

Returns:

Pangenome Index Name

pangenomeIndexName

@NotNull
public ImputePipelinePlugin pangenomeIndexName(@NotNull
                                                        java.lang.String value)

Set Pangenome Index Name. WARNING: By default the plugin will construct pangenome file and index names from the pangenomeHaplotypeMethod. Only use this parameter to over-ride that name with a different one. Be sure the pangenomeHaplotypeMethod matches the index.

Parameters:

value - Pangenome Index Name

Returns:

this plugin

indexKmerLength

public int indexKmerLength()

Minimap2 index parameter k, the kmer length of the minimizers, which is used to index the pangenome.

Returns:

Index Kmer Length

indexKmerLength

@NotNull
public ImputePipelinePlugin indexKmerLength(int value)

Set Index Kmer Length. Minimap2 index parameter k, the kmer length of the minimizers, which is used to index the pangenome.

Parameters:

value - Index Kmer Length

Returns:

this plugin

indexWindowSize

public int indexWindowSize()

Minimap2 index parameter w, the minimizer window size, which is used to index the pangenome.

Returns:

Index Window Size

indexWindowSize

@NotNull
public ImputePipelinePlugin indexWindowSize(int value)

Set Index Window Size. Minimap2 index parameter w, the minimizer window size, which is used to index the pangenome.

Parameters:

value - Index Window Size

Returns:

this plugin

indexNumberBases

@NotNull
public java.lang.String indexNumberBases()

Minimap2 index parameter I, the maximum number of bases loaded into memory, which is used to index the pangenome. This must be large enough to hold the entire pangenome in memory.

Returns:

Index Number Bases

indexNumberBases

@NotNull
public ImputePipelinePlugin indexNumberBases(@NotNull
                                                      java.lang.String value)

Set Index Number Bases. Minimap2 index parameter I, the maximum number of bases loaded into memory, which is used to index the pangenome. This must be large enough to hold the entire pangenome in memory.

Parameters:

value - Index Number Bases

Returns:

this plugin

minimapLocation

@NotNull
public java.lang.String minimapLocation()

Location of Minimap2 on file system. This defaults to use minimap2 if it is on the PATH environment variable.

Returns:

Location of Minimap2 Executable

minimapLocation

@NotNull
public ImputePipelinePlugin minimapLocation(@NotNull
                                                     java.lang.String value)

Set Location of Minimap2 Executable. Location of Minimap2 on file system. This defaults to use minimap2 if it is on the PATH environment variable.

Parameters:

value - Location of Minimap2 Executable

Returns:

this plugin

readMethod

@NotNull
public java.lang.String readMethod()

The read method name to used for the read mapping data stored in the DB.

Returns:

Read Method

readMethod

@NotNull
public ImputePipelinePlugin readMethod(@NotNull
                                                java.lang.String value)

Set Read Method. The read method name to used for the read mapping data stored in the DB.

Parameters:

value - Read Method

Returns:

this plugin

readMethodDescription

@Nullable
public java.lang.String readMethodDescription()

An additional description that will be stored with the read method name, if desired.

Returns:

Read Method Description

readMethodDescription

@NotNull
public ImputePipelinePlugin readMethodDescription(@NotNull
                                                           java.lang.String value)

Set Read Method Description. An additional description that will be stored with the read method name, if desired.

Parameters:

value - Read Method Description

Returns:

this plugin

outVcfFile

@NotNull
public java.lang.String outVcfFile()

The name of the file to be output by the PathsToVCFPlugin.

Returns:

Out Vcf File

outVcfFile

@NotNull
public ImputePipelinePlugin outVcfFile(@NotNull
                                                java.lang.String value)

Set Out Vcf File. The name of the file to be output by the PathsToVCFPlugin.

Parameters:

value - Out Vcf File

Returns:

this plugin

forceDBUpdate

public boolean forceDBUpdate()

Parameter to force the DB to update. If this is set to true and the DB is incompatible with the current PHG code, this will automatically update the DB if it can.

Returns:

Force D B Update

forceDBUpdate

@NotNull
public ImputePipelinePlugin forceDBUpdate(boolean value)

Set Force D B Update. Parameter to force the DB to update. If this is set to true and the DB is incompatible with the current PHG code, this will automatically update the DB if it can.

Parameters:

value - Force D B Update

Returns:

this plugin

liquibaseOutputDir

@NotNull
public java.lang.String liquibaseOutputDir()

The directory to which liquibase output files will be written.

Returns:

Liquibase Outdir

liquibaseOutputDir

@NotNull
public ImputePipelinePlugin liquibaseOutputDir(@NotNull
                                                        java.lang.String value)

Set Liquibase Outdir. The directory to which liquibase output files will be written.

Parameters:

value - Liquibase Outdir

Returns:

this plugin

skipLiquibaseCheck

public boolean skipLiquibaseCheck()

Should the liquibase check be skipped? Do not set to true if running inside a Docker. Then, only set to true if the PHG DB version is known to match the software version.

Returns:

Skip Liquibase Check

skipLiquibaseCheck

@NotNull
public ImputePipelinePlugin skipLiquibaseCheck(boolean value)

Set Skip Liquibase Check. Should the liquibase check be skipped? Do not set to true if running inside a Docker. Then, only set to true if the PHG DB version is known to match the software version.

Parameters:

value - Skip Liquibase Check

Returns:

this plugin

localGVCFFolder

@NotNull
public java.lang.String localGVCFFolder()

Folder where gvcfs will be downloaded and stored

Returns:

Local GVCF Folder

localGVCFFolder

@NotNull
public ImputePipelinePlugin localGVCFFolder(@NotNull
                                                     java.lang.String value)

Set Local GVCF Folder. Folder where gvcfs will be downloaded and stored

Parameters:

value - Local GVCF Folder

Returns:

this plugin