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PHG - Practical Haplotype Graph

Files of the artifact phg version 1.3 from the group net.maizegenetics.

Artifact phg
Group net.maizegenetics
Version 1.3
Last update 10. January 2023
Tags: practical haplotype graph
Organization not specified
URL https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/Home
License GNU Lesser General Public License, version 2.1
Dependencies amount 32
Dependencies log4j-core, guava, commons-math3, commons-codec, jfreechart, jfreesvg, ejml-ddense, trove4j, snappy-java, mail, json-simple, javax.json, sqlite-jdbc, htsjdk, ahocorasick, postgresql, colt, gs-core, tassel, kotlin-stdlib-jdk8, kotlin-script-runtime, fastutil, kotlinx-coroutines-core, biojava-core, biojava-genome, sshj, commons-io, jackson-module-kotlin, dataframe, protobuf-kotlin, protobuf-java, error_prone_annotations,
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Source code of phg version 1.3

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.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.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.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.CreateTestGenomes

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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