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- databaseName() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
- Database name
- databaseName(String) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
- Set Database Name.
- databaseName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
- Database name
- databaseName(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
- Set Database Name.
- DatabaseSummaryPlugin - class in net.maizegenetics.pangenome.db_loading
- dataSetReturned(PluginEvent) - function in net.maizegenetics.plugindef.AbstractPlugin
- dBConfig() - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
- Config file used to set up the db connection
- dBConfig(String) - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
- Set Db Config.
- dbConfigFile() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- File holding the DB config information
- dbConfigFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- Set Db Config File.
- dbConfigFile() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
- File holding the DB config information
- dbConfigFile(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
- Set Db Config File.
- dbConfigFile() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- File holding the DB config information
- dbConfigFile(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- Set Db Config File.
- dbConfigFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
- File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- dbConfigFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
- Set DB Config File.
- DBLoadingUtils - class in net.maizegenetics.pangenome.db_loading
- Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs.
- DBLoadingUtils.AnchorType - class in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- DBLoadingUtils.GenomeFileType - class in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- DBLoadingUtils.MethodType - class in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- DBVariant - class in net.maizegenetics.pangenome.api
- debugTaxon() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
- Debug taxon
- debugTaxon(String) - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
- Set Debug Taxon.
- decodeByteArrayToListOfVariantContext(Array) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- decodeByteArrayToVariantLongList(Array) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
- Method takes a Snappy compressed byte stream and decodes it into a List of Long objects
- decodeHapCountsArray(Array) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- decodeHapidList(Array) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- decodePathsArray(Array) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- decodePathsForMultipleLists(Array) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
- deleteMethodByName(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Takes a method name and deletes the entry for it from the methods table.
- deleteMethodByName(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Takes a method name and deletes the entry for it from the methods table.
- deletePaths(String,List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Deletes paths based on a method name and taxa.
- deletePaths(String,List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Deletes paths based on a method name and taxa.
- deletePathsById(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- deleteReadMappingPathsById(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Deletes from the read_mapping_paths table the ids in the ReadMappingIds List
- deleteReadMappingPathsById(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Deletes from the read_mapping_paths table the ids in the ReadMappingIds List
- deleteReadMappingsById(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Deletes from the read_mapping table based on the ids in the input List
- deleteReadMappingsById(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Deletes from the read_mapping table based on the ids in the input List
- deleteReadMappingsCascade(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Delete read_mappings from the read_mapping table based on provided ids.
- deleteReadMappingsCascade(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Delete read_mappings from the read_mapping table based on provided ids.
- deltafilter - enum entry in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT
- depth() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
- displayString() - function in net.maizegenetics.pangenome.api.AlleleInfo
- distanceAllTaxaToGivenTaxa(DistanceMatrix,String) - function in net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
- distanceCalculation() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- Distance calculation type
- distanceCalculation(DistanceCalculation) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- Set Distance Calculation.
- distanceFromSNPs(RangeMap,RangeMap) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
- distanceTaxaPair(DistanceMatrix,String,String) - function in net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
- distributionTaxaRepresented(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.GraphUtils
- dockerCmd() - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
- The docker command name.
- dockerCmd(String) - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
- Set Docker Command.
- dockerDir() - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
- Directory path where the file 'Dockerfile' exists for creating the PHG Postgresql docker
- dockerDir(String) - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
- Set Docker Directory.