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PHG - Practical Haplotype Graph

Files of the artifact phg version 1.10 from the group net.maizegenetics.

Artifact phg
Group net.maizegenetics
Version 1.10
Last update 20. August 2024
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 1.10

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.io
net.maizegenetics.pangenome.io.net.maizegenetics.pangenome.io.Haplotypegraph
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.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.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_info.xml
phg.phg.tassel_menu.xml




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