| Package | Description |
|---|---|
| net.maizegenetics.pangenome.db_loading | |
| net.maizegenetics.pangenome.processAssemblyGenomes |
| Class and Description |
|---|
| AnchorDataPHG
THis class differs from AnchorData in WGS_whatever as it
includes more fields to match what is stored in PHGSchema's
anchor_haplotypes.
|
| CreateIntervalBedFilesPlugin
Created by zrm22 on 1/16/18.
|
| CreateIntervalsFileFromGffPlugin
This class creates the interval files needed for running GATK haplotype caller,
and the csv files needed for loading reference sequence into the database.
|
| CreatePHGPostgresDockerPlugin
This plugin will create the phg_postgres docker if it doesn't exist.
|
| DBLoadingUtils.AnchorType |
| DBLoadingUtils.MethodType |
| GeneGFFData |
| GenoHaploData
Object to hold data needed to populate the genotypes and haplotypes tables.
|
| GetDBConnectionPlugin
Plugin takes a configFile with db specifics and a boolean indicating whether
a new db shoudl be created.
|
| LoadConsensusAnchorSequencesPlugin
This method takes an input file in fasta format and adds the sequences
to the data base.
|
| LoadGenomeIntervalsToPHGdbPlugin
Before running this plugin, GetDBConnectionPlugin must be run.
|
| LoadHaplotypeCountsTablePlugin
This method reads haplotype counts from an incoming DataSet object, and stores results to a specified database.
|
| LoadHapSequencesFromGVCFPlugin
Plugin which will upload a GVCF file to the DB.
|
| LoadHapSequencesToDBPlugin
This method takes data processed through GATK haplotype caller, or through
processAssebmlyGenomes.Minimap2PipelinePlugin.
|
| PHGData |
| PHGDataWriter |
| SplitFastaByChromPlugin
Splits fasta by chromosome.
|
| Class and Description |
|---|
| AnchorDataPHG
THis class differs from AnchorData in WGS_whatever as it
includes more fields to match what is stored in PHGSchema's
anchor_haplotypes.
|
| DBLoadingUtils.AnchorType |
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