Package net.maizegenetics.pangenome.pipelineTests
See: Description
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Class Summary Class Description CompareToKnownSNPPlugin Plugin to compare A GenotypeTable to a known trusted GenotypeTable Inputs: -DataSet of at least 2 GenotypeTables, First one is the known SNP set you wish to compare to, the rest are compared in order. GenerateRForPHG This class holds methods and classes to generate R code for PHG classes. HaplotypesDataVectors Class that holds data for haplotypes in a graph in vector form HaplotypesDataMetricsPlugin Code to provide metrics on PHG haplotypes based on user supplied method. ContrastHaplotypeAndAssemblySequence Integration test to evaluate fasta file generated from GVCF files for the whole genome against assembly fasta Assembly fasta Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (W22). EvaluateHaplotypeFastaInKnownIBDRegions Unit test to evaluate fasta file generated from GVCF files for anchors in IBD regions to B73 Get all the anchorIDs in the IBD region of chromosome 10 Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (alternative). CountNsInRawHapSequencesPlugin NOTE: THis test is obsolete - uses old schema and old connection method. FindProteomeGenesInAssembly NOTE: Needs to be re-worked with new db. RefRangeVectors This class creates a range of vectors holding data for PHG ReferenceRange objects