A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W
W
- wasCancelled() - function in net.maizegenetics.plugindef.AbstractPlugin
- weightedMax(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
- weightedSum(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
- wgsDepth() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Depth for WGS
- wgsDepth(Double) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Set WGS Depth.
- windowSize() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- Window size to add to the extendedBedFile
- windowSize(Integer) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
- Set Window Size.
- writeDataToFile(List,String,int,BufferedWriter) - function in net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
- writeDelimitedTo(OutputStream) - function in com.google.protobuf.AbstractMessageLite
- writeFasta(HaplotypeGraph,String) - function in net.maizegenetics.pangenome.api.GraphIO
- Writes given graph to fasta format.
- WriteFastaFromGraphPlugin - class in net.maizegenetics.pangenome.api
- writeGraphInfoAllChr(String,Array,HaplotypeGraph,Array,String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
- writeGraphInfoFilesForChr(String,List,HaplotypeGraph,Multimap,Chromosome,String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- writeGraphInfoFilesForChr(String,Array,HaplotypeGraph,Map,Map,Chromosome,String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
- writePathInformation(String,List,HaplotypeGraph,Multimap) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- Method is used to write diagnostic information about a path to a file.
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
- writeTo(CodedOutputStream) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
- writeVariantContextsToVCF(List,String,String,String) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
- Method to write the list of VariantContexts out to a vcf file.
- writeVariantContextsToVCF(List,String,String,List) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils