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- bamFile() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
- File Name of the bam file
- bamFile(String) - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
- Set Bam File.
- baseDirectory() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- The base directory for the small genomes data.
- baseDirectory(String) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Set Base Dir.
- baseString() - function in net.maizegenetics.pangenome.api.AlleleInfo
- bedFile() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- Name for the bed file
- bedFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- Set Bed File.
- bedFile() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
- Bed file containing the gene information.
- bedFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
- Set Bed File.
- bfInfoFilename() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- The name of the file to node probabilities from the backward-forward algorithm will be written.
- bfInfoFilename(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- Set Bf Info File.
- BOTH - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType
- build() - function in com.google.protobuf.MessageLite.Builder
- build() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
- build() - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
- build() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
- buildPartial() - function in com.google.protobuf.MessageLite.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
- buildPartial() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
- byteArrayToLongList(Array) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils