Package net.maizegenetics.pangenome.pipelineTests

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.
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).
CountConsensusTaxaAtRefRange	This class counts the number of taxa represented at each genome_interval region based on the method supplied.
CountNsInRawHapSequencesPlugin	Calculates the percentage of N's for each "raw" haplotype (ie, not consensus) for each genome interval (anchor, not inter-anchors).
EvaluateGVCFbyKnownSNPTest	Create unit test to evaluate GVCF SNPs by comparing to known SNPs.
EvaluateGVCFbyKnownSNPTest2	Create unit test to evaluate GVCF SNPs by comparing to known SNPs.
EvaluateGVCFWithIBDTest	Evaluate GVCF calls in regions with IBD to the reference genome.
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).
FindProteomeGenesInAssembly	NOTE: Needs to be re-worked with new db.
SimpleGVCFReader	Created by edbuckler on 6/22/17.