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Genomic variants interpretation toolkit

Files of the artifact variant-spark_2.11 version 0.4.0 from the group au.csiro.aehrc.variant-spark.

Artifact variant-spark_2.11
Group au.csiro.aehrc.variant-spark
Version 0.4.0
Last update 13. June 2022
Tags: genomic interpretation toolkit variants
Organization not specified
URL http://bioinformatics.csiro.au/variantspark
License CSIRO Non-Commercial Source Code Licence Agreement v1.0
Dependencies amount 8
Dependencies graph-core_${scala.binary.version}, fastutil, scala-csv_${scala.binary.version}, htsjdk, joda-time, args4j, json4s-ext_${scala.binary.version}, dsiutils,
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Source code of variant-spark_2.11 version 0.4.0

META-INF
META-INF.META-INF.MANIFEST.MF
META-INF.maven.au.csiro.aehrc.variant-spark.variant-spark_2.11
META-INF.maven.au.csiro.aehrc.variant-spark.variant-spark_2.11.META-INF.maven.au.csiro.aehrc.variant-spark.variant-spark_2.11.pom.properties
META-INF.maven.au.csiro.aehrc.variant-spark.variant-spark_2.11.META-INF.maven.au.csiro.aehrc.variant-spark.variant-spark_2.11.pom.xml
au.csiro.pbdava.ssparkle.common.arg4j
au.csiro.pbdava.ssparkle.common.arg4j.au.csiro.pbdava.ssparkle.common.arg4j.AppRunner.scala
au.csiro.pbdava.ssparkle.common.arg4j.au.csiro.pbdava.ssparkle.common.arg4j.AppRunner2.scala
au.csiro.pbdava.ssparkle.common.arg4j.au.csiro.pbdava.ssparkle.common.arg4j.TestArgs.scala
au.csiro.pbdava.ssparkle.common.utils
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.CSVUtils.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.FastUtilConversions.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.LoanUtils.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.Logging.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.MiscUtils.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.Prof.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.ReusablePrintStream.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.SerialUtils.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.Timed.scala
au.csiro.pbdava.ssparkle.common.utils.au.csiro.pbdava.ssparkle.common.utils.VersionInfo.scala
au.csiro.pbdava.ssparkle.spark
au.csiro.pbdava.ssparkle.spark.au.csiro.pbdava.ssparkle.spark.SparkApp.scala
au.csiro.pbdava.ssparkle.spark.au.csiro.pbdava.ssparkle.spark.SparkUtils.scala
au.csiro.sparkle.cmd
au.csiro.sparkle.cmd.au.csiro.sparkle.cmd.CmdApp
au.csiro.sparkle.cmd.au.csiro.sparkle.cmd.DefaultObjectFactory
au.csiro.sparkle.cmd.au.csiro.sparkle.cmd.MultiCmdApp
au.csiro.sparkle.common
au.csiro.sparkle.common.au.csiro.sparkle.common.LoanUtils
au.csiro.sparkle.common.au.csiro.sparkle.common.ObjectFactory
au.csiro.sparkle.common.au.csiro.sparkle.common.ObjectProvider
au.csiro.sparkle.common.au.csiro.sparkle.common.ScalaUtils
au.csiro.sparkle.common.au.csiro.sparkle.common.ThrowingConsumer
au.csiro.sparkle.common.au.csiro.sparkle.common.ThrowingFunction
au.csiro.sparkle.common.args4j
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.ArgsApp
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.ArgsObjectFactory
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.DateOptionHandler
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.HasUsage
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.IntListOptionHandler
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.ObjectOptionHandler
au.csiro.sparkle.common.args4j.au.csiro.sparkle.common.args4j.RegisterHandlers
au.csiro.sparkle.spark
au.csiro.sparkle.spark.au.csiro.sparkle.spark.AppContext
au.csiro.sparkle.spark.au.csiro.sparkle.spark.Counter
au.csiro.sparkle.spark.au.csiro.sparkle.spark.Long2LongAccumulableParam
au.csiro.sparkle.spark.au.csiro.sparkle.spark.SparkTask
au.csiro.sparkle.spark.au.csiro.sparkle.spark.SparkUtils
au.csiro.sparkle.spark.au.csiro.sparkle.spark.SparkleJavaApp
au.csiro.variantspark.algo
au.csiro.variantspark.algo.au.csiro.variantspark.algo.ArrayOps
au.csiro.variantspark.algo.au.csiro.variantspark.algo.DecisionTree.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.GiniImpurity.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.Impurity.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.PairwiseOperation.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.PredictiveModel.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.RandomForest.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.Split.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.StdTreeFeatures.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.TreeFeature.scala
au.csiro.variantspark.algo.au.csiro.variantspark.algo.WideKMeans.scala
au.csiro.variantspark.algo.impurity
au.csiro.variantspark.algo.impurity.au.csiro.variantspark.algo.impurity.FastGini
au.csiro.variantspark.algo.impurity.au.csiro.variantspark.algo.impurity.GiniImpurityAggregator
au.csiro.variantspark.algo.impurity.au.csiro.variantspark.algo.impurity.VarianceImpurityAggregator
au.csiro.variantspark.algo.metrics
au.csiro.variantspark.algo.metrics.au.csiro.variantspark.algo.metrics.Metrics.scala
au.csiro.variantspark.algo
au.csiro.variantspark.algo.au.csiro.variantspark.algo.package.scala
au.csiro.variantspark.algo.split
au.csiro.variantspark.algo.split.au.csiro.variantspark.algo.split.AbstractIndexedSplitterBase
au.csiro.variantspark.algo.split.au.csiro.variantspark.algo.split.JNaiveContinousIndexedSplitter
au.csiro.variantspark.algo.split.au.csiro.variantspark.algo.split.JOrderedFastIndexedSplitter
au.csiro.variantspark.algo.split.au.csiro.variantspark.algo.split.JOrderedIndexedSplitter
au.csiro.variantspark.api
au.csiro.variantspark.api.au.csiro.variantspark.api.AnalyticsFunctions.scala
au.csiro.variantspark.api.au.csiro.variantspark.api.CommonPairwiseOperation.scala
au.csiro.variantspark.api.au.csiro.variantspark.api.ImportanceAnalysis.scala
au.csiro.variantspark.api.au.csiro.variantspark.api.VSContext.scala
au.csiro.variantspark.api.au.csiro.variantspark.api.package.scala
au.csiro.variantspark.cli
au.csiro.variantspark.cli.au.csiro.variantspark.cli.AnalyzeRFCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.BuildVarIndexCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.CochranArmanCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.ConvertCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.FilterCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.GenerateFeaturesCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.GenerateLabelsCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.GenerateLabelsNoiseCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.ImportanceCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.NullImportanceCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.PairWiseDistanceCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.PredictCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.TestCmd.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.VariantSparkApp.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.VcfToLabels.scala
au.csiro.variantspark.cli.au.csiro.variantspark.cli.VersionCmd.scala
au.csiro.variantspark.cli.args
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.FeatureSourceArgs.scala
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.ImportanceArgs.scala
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.LabelSourceArgs.scala
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.ModelOutputArgs.scala
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.RandomForestArgs.scala
au.csiro.variantspark.cli.args.au.csiro.variantspark.cli.args.SparkArgs.scala
au.csiro.variantspark.cmd
au.csiro.variantspark.cmd.au.csiro.variantspark.cmd.EchoUtils.scala
au.csiro.variantspark.cmd.au.csiro.variantspark.cmd.Echoable.scala
au.csiro.variantspark.data
au.csiro.variantspark.data.au.csiro.variantspark.data.Data.scala
au.csiro.variantspark.data.au.csiro.variantspark.data.Feature.scala
au.csiro.variantspark.data.au.csiro.variantspark.data.Representation.scala
au.csiro.variantspark.data.au.csiro.variantspark.data.StdData.scala
au.csiro.variantspark.data.au.csiro.variantspark.data.VariableType.scala
au.csiro.variantspark.data.au.csiro.variantspark.data.package.scala
au.csiro.variantspark.external
au.csiro.variantspark.external.au.csiro.variantspark.external.Model.scala
au.csiro.variantspark.external.au.csiro.variantspark.external.ModelConverter.scala
au.csiro.variantspark.hail.methods
au.csiro.variantspark.hail.methods.au.csiro.variantspark.hail.methods.RFModel.scala
au.csiro.variantspark.input
au.csiro.variantspark.input.au.csiro.variantspark.input.CsvFeatureSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.CsvLabelSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.CsvStdFeatureSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.FeatureSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.HashingLabelSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.ImputationStrategy.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.LabelSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.ParquetFeatureSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.VCFFeatureSource.scala
au.csiro.variantspark.input.au.csiro.variantspark.input.VCFSource.scala
au.csiro.variantspark.input.generate
au.csiro.variantspark.input.generate.au.csiro.variantspark.input.generate.EffectLabelGenerator.scala
au.csiro.variantspark.input.generate.au.csiro.variantspark.input.generate.NoisyEffectLabelGenerator.scala
au.csiro.variantspark.input.generate.au.csiro.variantspark.input.generate.OrdinalFeatureGenerator.scala
au.csiro.variantspark.metrics
au.csiro.variantspark.metrics.au.csiro.variantspark.metrics.Gini.scala
au.csiro.variantspark.metrics.au.csiro.variantspark.metrics.Metrics.scala
au.csiro.variantspark.output
au.csiro.variantspark.output.au.csiro.variantspark.output.CSVFeatureSink.scala
au.csiro.variantspark.output.au.csiro.variantspark.output.CSVFeatureSink2.scala
au.csiro.variantspark.output.au.csiro.variantspark.output.FeatureSink.scala
au.csiro.variantspark.output.au.csiro.variantspark.output.ParquetFeatureSink.scala
au.csiro.variantspark.python
au.csiro.variantspark.python.au.csiro.variantspark.python.Metadata.scala
au.csiro.variantspark.stats
au.csiro.variantspark.stats.au.csiro.variantspark.stats.CochranArmitageTest
au.csiro.variantspark.stats.au.csiro.variantspark.stats.CochranArmitageTestCalculator.scala
au.csiro.variantspark.tests
au.csiro.variantspark.tests.au.csiro.variantspark.tests.TestWideDecisionTree.scala
au.csiro.variantspark.tests.au.csiro.variantspark.tests.TestWideKMeans.scala
au.csiro.variantspark.utils
au.csiro.variantspark.utils.au.csiro.variantspark.utils.ArraysUtils
au.csiro.variantspark.utils.au.csiro.variantspark.utils.CV.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.FactorVariable.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.HdfsPath.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.MurMur3Hash
au.csiro.variantspark.utils.au.csiro.variantspark.utils.Projection.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.Sampling.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.VectorRDDFunction.scala
au.csiro.variantspark.utils.au.csiro.variantspark.utils.package.scala
au.csiro.variantspark.work
au.csiro.variantspark.work.au.csiro.variantspark.work.AnyValTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.BitsetTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.BreezeTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.CaseTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.DataSetTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.ImplicitTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.JSONTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.ObjectTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.RandomnesTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.RegexTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.StreamTest.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.Test.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.TestApp.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.TestMax.scala
au.csiro.variantspark.work.au.csiro.variantspark.work.VcfReaderTest.scala
ref-contigs
ref-contigs.ref-contigs.b37.vcf




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