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    Download phg JAR 0.0.34 with all dependencies


    Files of the artifact phg version 0.0.34 from the group net.maizegenetics.

    Artifact phg
    Group net.maizegenetics
    Version 0.0.34


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    Source code of phg version 0.0.34

    META-INF
    META-INF.META-INF.MANIFEST.MF
    net.maizegenetics.pangenome
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.CompareFastaToReference
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.CompareHaplotypesToAssembly
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.GVCFStats
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
    net.maizegenetics.pangenome.net.maizegenetics.pangenome.GetFastaSequenceLengths
    net.maizegenetics.pangenome.Utils
    net.maizegenetics.pangenome.Utils.net.maizegenetics.pangenome.Utils.CreateHashForFiles
    net.maizegenetics.pangenome.api
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.AlleleInfo
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.CreateGraphUtils
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.DBVariant
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.FilterGraphPlugin
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.GraphIO
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.GraphUtils
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypeEdge
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypeGraph
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypeNode
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypePath
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.HaplotypeSequence
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.MethodTableReportPlugin
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.PHG_mock_db_for_api_unit_test.sql
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.RMethods
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.ReferenceRange
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.Variant
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.VariantUtils
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
    net.maizegenetics.pangenome.api.net.maizegenetics.pangenome.api.api_loaddb_unit_test.db
    net.maizegenetics.pangenome.db_loading
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.AnchorDataPHG
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.DBLoadingUtils
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.GeneGFFData
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.GenoHaploData
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.PHGData
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.PHGDataWriter
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.PHGPostgreSQLSchema.sql
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.PHGSchema.sql
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.PHGdbAccess
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.TestPHGStuff
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.VariantMappingData
    net.maizegenetics.pangenome.db_loading.net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
    net.maizegenetics.pangenome.fastaExtraction
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.ExtractFastaUtils
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
    net.maizegenetics.pangenome.fastaExtraction.net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
    net.maizegenetics.pangenome.gui
    net.maizegenetics.pangenome.gui.net.maizegenetics.pangenome.gui.CreateStreamGraph
    net.maizegenetics.pangenome.gui.net.maizegenetics.pangenome.gui.ViewGraphPlugin
    net.maizegenetics.pangenome.gvcfFiltering
    net.maizegenetics.pangenome.gvcfFiltering.net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
    net.maizegenetics.pangenome.gvcfFiltering.net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
    net.maizegenetics.pangenome.gvcfFiltering.net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
    net.maizegenetics.pangenome.gvcfFiltering.net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
    net.maizegenetics.pangenome.gvcfFiltering.net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
    net.maizegenetics.pangenome.hapCalling
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.FastqKmerToHapCountPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.HapCallingUtils
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
    net.maizegenetics.pangenome.hapCalling.net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
    net.maizegenetics.pangenome.hapcollapse
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.GVCFUtils
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.RefAltData
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
    net.maizegenetics.pangenome.hapcollapse.net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
    net.maizegenetics.pangenome.multiSequenceAlignment
    net.maizegenetics.pangenome.multiSequenceAlignment.net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
    net.maizegenetics.pangenome.multiSequenceAlignment.net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
    net.maizegenetics.pangenome.multiSequenceAlignment.net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
    net.maizegenetics.pangenome.pipelineTests
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFWithIBDTest
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.FindProteomeGenesInAssembly
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.HaplotypesDataVectors
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
    net.maizegenetics.pangenome.pipelineTests.net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
    net.maizegenetics.pangenome.processAssemblyGenomes
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.RedirectStreams
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
    net.maizegenetics.pangenome.processAssemblyGenomes.net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors
    net.maizegenetics.pangenome.smallseq
    net.maizegenetics.pangenome.smallseq.net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
    net.maizegenetics.pangenome.smallseq.net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPluginTest
    net.maizegenetics.pangenome.smallseq.net.maizegenetics.pangenome.smallseq.CreateTestGenomes
    net.maizegenetics.pangenome.smallseq.net.maizegenetics.pangenome.smallseq.RunSmallSeqTestsDocker
    net.maizegenetics.pangenome.smallseq.net.maizegenetics.pangenome.smallseq.SmallSeqPaths
    net.maizegenetics.pangenome.trimAnchors
    net.maizegenetics.pangenome.trimAnchors.net.maizegenetics.pangenome.trimAnchors.AnchorInfo
    net.maizegenetics.pangenome.trimAnchors.net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors
    phg
    phg.phg.tassel_menu.xml




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