Package net.maizegenetics.pangenome.db_loading
See: Description
-
Enum Summary Enum Description AnchorType MethodType GenomeFileType -
Class Summary Class Description DBLoadingUtils Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs. CreatePHGPostgresDockerPlugin This plugin will create the phg_postgres docker if it doesn't exist. GenoHaploData Object to hold data needed to populate the genotypes and haplotypes tables. VariantMappingData Class created to store Variant mapping data for populating the variants PHG table. GetDBConnectionPlugin Plugin takes a configFile with db specifics and a boolean indicating whether a new db shoudl be created. GeneGFFData CreateIntervalBedFilesPlugin Created by zrm22 on 1/16/18. CreateBiggerIntervals VariantsProcessingUtils This class contains methods to aid in processing a VariantContext list into the PHG db variants, alleles, and haplotypes tables FindTrimmedAssemblyCoordinates THis file is similar to FindTrimmedAnchorCoordinates used for the reference. 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. AddRefRangeAsAssemblyPlugin This function is fairly obsolete. CreateGeneIntervalsFromConservedGFFPlugin Creates bed file with chromosome and coordinates to be used to create PHG reference ranges. DatabaseSummaryPlugin AddRefRangeGroupPlugin This class creates a user defined ref range group, adds it to the specified db, associates requested reference ranges with the new group. CloseDBConnectionPlugin This method closes a DB connection. SplitFastaByChromPlugin Splits fasta by chromosome. PHGdbAccess Access methods for postgres or SQL PHG dbs. FindTrimmedAnchorCoordinates NOTE: This version works on the REF only. 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. CreateIntervalsFile This method must be re-worked - getHaplotypeAnchorCoordinates no longer accesses the correct tables. 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. TestPHGStuff ShellScript_createLoadHaplotypes Takes a list of fasta file, creates a chell script to load them. AnchorDataPHG THis class differs from AnchorData in WGS_whatever as it includes more fields to match what is stored in PHGSchema's anchor_haplotypes. -
Interface Summary Interface Description PHGDataWriter PHGData