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- old(Array) - function in net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
- otherData() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData
- outFile() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
- Output file directory name, or new directory path; Directory will be created, if doesn't exist.
- outFile(String) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
- Set Donor dir/file basename.
- output() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
- File Name of the filtered read output
- output(String) - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
- Set Output File.
- outputBase() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
- base name for output files from this Plugin.
- outputBase(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
- Set Output file base.
- outputDir() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
- Directory where output files will be written
- outputDir(String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
- Set Output Directory.
- outputDir() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
- Path to write the split files
- outputDir(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
- Set Output Directory.
- outputDir() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
- Directory to hold the output files.
- outputDir(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
- Set Output Dir.
- outputDir() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
- Output Directory
- outputDir(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
- Set Output Dir.
- outputDir() - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
- Directory where you want to store the output VCFs
- outputDir(String) - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
- Set Output Dir.
- outputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
- Output directory including trailing / for writing files
- outputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
- Set Output Directory.
- outputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
- Output fastq file to use as input for BWA-MEM
- outputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
- Set Output File.
- outputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
- Output directory including trailing / for writing files
- outputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
- Set Output Directory.
- outputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
- Output directory including trailing / for writing files
- outputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
- Set Output Directory.
- outputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
- Output Directory
- outputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
- Set Output Directory.
- outputFile() - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
- Output filename
- outputFile(String) - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
- Set Output File.
- outputFile() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
- Name of output file to be written
- outputFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
- Set Output File.
- outputFile() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
- Output GVCF File Path and Name.
- outputFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
- Set Output G V C F File.
- outputFile() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
- FUll path to output file created by this plugin .
- outputFile(String) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
- Set Output File.
- outputFile() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
- Output File
- outputFile(String) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
- Set Output File.
- outputFile() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
- FUll path to output file created by this plugin .
- outputFile(String) - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
- Set Output File.
- outputFileDirectory() - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
- Output file directory
- outputFileDirectory(String) - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
- Set Output File Directory.
- outputFileName() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
- Name of output file
- outputFileName(String) - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
- Set Output File.
- outputVCFDir() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Output VCF file directory.
- outputVCFDir(String) - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Set Output VCF Directory.