Package net.maizegenetics.pangenome.db_loading

Interface Summary

Interface	Description
PHGData
PHGDataWriter

Class Summary

Class	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.
CloseDBConnectionPlugin	This method closes a DB connection.
CreateAnchorFilesFromGeneGFF	Based on WGS_whatever.CreateAnchorsFromGeneGff.java This method creates two fasta files of anchor coordinates: The first has exact gene coordinates to be used when blasting B73 reference genes against a particular assembly, e.g.
CreateBiggerIntervals
CreateCSV_TrimmedAnchorLoading	This method takes as input 2 csv files It takes the data from FindTrimmedAnchorCoordinates.jar, then calculates new coordinates using the old ref coordinates CSV file used for loading.
CreateIntervalBedFilesPlugin	Created by zrm22 on 1/16/18.
CreateIntervalsFile	This method must be re-worked - getHaplotypeAnchorCoordinates no longer accesses the correct tables.
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	Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs.
FindTrimmedAnchorCoordinates	NOTE: This version works on the REF only.
FindTrimmedAssemblyCoordinates	THis file is similar to FindTrimmedAnchorCoordinates used for the reference.
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.
PHGdbAccess	Access methods for postgres or SQL PHG dbs.
ShellScript_createLoadHaplotypes	Takes a list of fasta file, creates a chell script to load them.
SplitFastaByChromPlugin	Splits fasta by chromosome.
TestPHGStuff

Enum Summary

Enum	Description
DBLoadingUtils.AnchorType
DBLoadingUtils.MethodType