├── .github └── workflows │ ├── ci.yml │ └── publish-release.yml ├── .gitignore ├── .pydevproject ├── .readthedocs.yml ├── .scalafmt.conf ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── THIRDPARTY ├── bin ├── find-varspark-jar ├── jvariant-spark └── variant-spark ├── cloud ├── aws-emr │ ├── README.md │ ├── bootstrap │ │ ├── install-hail.sh │ │ ├── install-jupyter-emr5.sh │ │ ├── install-jupyter-noNotebook.sh │ │ ├── install-jupyter.sh │ │ ├── install-variant-spark.sh │ │ └── s3-bootstrap.sh │ ├── cf-templates │ │ ├── README.md │ │ ├── VariantSpark_Hail_EMR_Notebook.yaml │ │ ├── VariantSpark_Hail_EMR_Step.yaml │ │ ├── VariantSpark_example_with_Hail_library.ipynb │ │ ├── emr-roles.yaml │ │ ├── notes.md │ │ └── template.yaml │ ├── conf │ │ ├── config.max.yaml │ │ └── config.min.yaml │ └── python │ │ ├── LICENSE.txt │ │ ├── MANIFEST.in │ │ ├── setup.cfg │ │ ├── setup.py │ │ └── vs_emr │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── config │ │ └── config.min.yaml │ │ └── templates │ │ └── spot-cluster.yaml └── databricks │ ├── notebooks-databricks-aws │ ├── VS_HipsterIndex_Spark2.2-with-graphics.scala │ ├── VariantSpark_HipsterIndex_Spark2.1.scala │ └── VariantSpark_HipsterIndex_Spark2.2.scala │ └── notebooks-databricks-azure │ ├── VS_HipsterIndex_Spark2.2-with-graphics.scala │ ├── VariantSpark_HipsterIndex_Spark2.2.scala │ ├── run_importance_chr22.ipynb │ └── run_importance_chr22_with_hail.ipynb ├── conf └── log4j.properties ├── contributions ├── AwsMarketplace │ ├── Figs │ │ ├── ss01-MarketplaceHome.png │ │ ├── ss02-Subscribe.png │ │ ├── ss03-Region.png │ │ ├── ss04-Action.png │ │ ├── ss05-CloudFormation.png │ │ ├── ss06-Parameter.png │ │ ├── ss07-Create.png │ │ ├── ss08-StackEventStart.png │ │ ├── ss09-StackEventCompelete.png │ │ ├── ss10-StackInfo.png │ │ ├── ss11-StackResource.png │ │ ├── ss12-StackParameter.png │ │ ├── ss13-StackOutput.png │ │ ├── ss14-EMR.png │ │ ├── ss14-EMRBootstrap.png │ │ ├── ss14-EMRConfig.png │ │ ├── ss15-Ganglia.png │ │ ├── ss16-S3Bucket.png │ │ ├── ss17-Jupyter.png │ │ ├── ss18-Notebook.png │ │ ├── ss19-Run.png │ │ ├── ss20-Manhattan.png │ │ ├── ss21-GangliaActive.png │ │ ├── ss22-StackDeleteConfirm.png │ │ ├── ss23-StackDeletion.png │ │ └── ss24-StackDeleteCompeleted.png │ └── README.md ├── JsonRfAnalyser │ ├── Hipster2.csv │ ├── JsonRfAnalyser.py │ ├── README.md │ ├── RF.json.gz │ ├── output.tar.gz │ ├── runTest.sh │ └── ss.png ├── PValues │ ├── README.md │ ├── data │ │ └── chr22_22_16050408-model.json │ └── model2counts.py └── WebVisualiser │ ├── README.md │ ├── jquery-1.7.1.min.js │ ├── rf.json │ ├── rfview.css │ ├── rfview.html │ ├── rfview.js │ └── vis-network.js ├── data ├── CNAE-9-labels.csv ├── CNAE-9-wide.csv ├── CNAE-9.csv ├── README.md ├── ch22-model.ser ├── chr22-labels-hail.csv ├── chr22-labels.csv ├── chr22_1000.csv ├── chr22_1000.vcf ├── chr22_1000.vcf.bgz ├── chr22_1000.vcf.bz2 ├── chr22_1000.vcf.gz ├── chr22_1000_GRCh38.vcf ├── chr22_1000_full_pheno.csv ├── chr22_1000_missing.vcf ├── chr22_1000_pheno-wide.csv ├── chr22_1000_pheno.csv ├── har_aal.csv.bz2 ├── har_aal_labels.csv ├── hipsterIndex │ ├── hipster.vcf.bgz │ ├── hipster_labels.txt │ └── hipster_labels_covariates.txt ├── importance-chr22-HG00097.csv ├── ranger-labels_10000.csv ├── ranger-types.csv └── ranger-wide_1000_10000.csv.bz2 ├── dev ├── IntelJ-inspections.xml ├── Notes.md ├── README-hail.md ├── README.md ├── build.sh ├── dev-requirements.txt ├── make_dist.sh ├── misc-deploy-hail-to-maven.sh ├── misc-snapshot-release.sh ├── py-dist.sh ├── py-docs.sh ├── py-lint.sh ├── py-pypi.sh ├── py-setup.sh ├── py-test.sh ├── py-zip.sh ├── rtd-requirements.txt ├── scalafmt.sh ├── test-gen-hail-cases.sh ├── test-gen-regression-cases.sh ├── test-gen-stats-cases.sh ├── test-gen-synth-data.sh ├── test-set-travis-env.sh ├── test-travis.sh ├── travis-build.sh ├── travis-prepare-s3-release.sh └── travis-set-ver.sh ├── docs ├── index.html └── notebook-examples │ ├── VariantSpark_HipsterIndex.html │ ├── VariantSpark_HipsterIndex_Spark1.6.html │ ├── VariantSpark_HipsterIndex_Spark2.html │ ├── VariantSpark_HipsterIndex_Spark2_DB5.3.html │ └── VariantSpark_HipsterIndex_Spark2_DB5.5.html ├── examples ├── command-line │ ├── local_run-importance-ch22.sh │ ├── local_run-importance-ch22_with_pheno.sh │ ├── local_run-importance-har_all.sh │ ├── local_run-importance-it.sh │ ├── local_run-importance-ranger.sh │ ├── local_run-predict-ch22.sh │ ├── run_importance_chr22.ipynb │ ├── run_importance_chr22_with_hail.ipynb │ ├── yarn_run-importance-ch22.sh │ └── yarn_run-importance-ranger.sh └── notebooks │ ├── HipsterHailvsVS.ipynb │ ├── HipsterHailvsVS_covariates.ipynb │ ├── VariantSpark_HipsterIndex_Spark2.1.scala │ ├── VariantSpark_HipsterIndex_Spark2.2.scala │ ├── compute_local_fdr.ipynb │ └── run_importance_chr22.ipynb ├── images ├── AWS-EMR-VariantSpark.png ├── YOW__Conference_2017_Lynn_Langit___Denis_Bauer_-_Cloud_Data_Pipelines_-_YouTube.png └── vs-spark-summit-2017.png ├── perf ├── local-perf-ranger_100.sh ├── local-perf-ranger_900.sh ├── run-importance-ranger_135000.sh ├── run-importance-ranger_135000_1000t.sh ├── run-importance-ranger_135000_100t.sh ├── run-importance-ranger_135000_100t_sp32.sh ├── run-importance-ranger_15000.sh ├── run-importance-ranger_5000.sh ├── slocal-perf-ranger_100.sh └── slocal-perf-ranger_900.sh ├── pom.xml ├── private ├── R │ └── hip-analyze_permutations.R ├── README.md ├── gen-features.sh ├── gen-importance.sh ├── gen-labels.sh ├── local-gen-convert.sh ├── local-gen-features.sh ├── local-gen-importance.sh ├── local-gen-labels.sh ├── local-run-importance-ch22.sh ├── local-run-importance-ranger.sh ├── local_run-importance-ch22.sh ├── local_run-importance-hipster.sh ├── local_run-null-importance-ch22.sh ├── local_run-null-importance-hipster.sh ├── run-importance-ch22.sh └── run-importance-ranger.sh ├── python ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs │ ├── Makefile │ ├── _section.rst │ ├── cmd_ref.rst │ ├── conf.py │ ├── development.rst │ ├── examples │ │ ├── run_importance_chr22.ipynb │ │ └── run_importance_chr22_with_hail.ipynb │ ├── getting_started.rst │ ├── index.rst │ ├── pyapi.rst │ ├── varspark.core.rst │ ├── varspark.hail.rst │ ├── varspark.rst │ └── varspark.utils.rst ├── examples │ ├── chr21_GRCh38_hail.py │ ├── chr21_missing_hail.py │ ├── hipster_index.py │ ├── hipster_index_hail.py │ └── hipster_index_hail_covariates.py ├── pylintrc ├── pytest.ini ├── readme_pvalues.md ├── requirements.txt ├── setup.cfg ├── setup.py └── varspark │ ├── __init__.py │ ├── cli.py │ ├── core.py │ ├── etc.py │ ├── hail │ ├── __init__.py │ ├── context.py │ ├── hail.py │ ├── lfdrvs.py │ ├── methods.py │ ├── plot.py │ └── rf.py │ ├── java.py │ ├── lang.py │ ├── stats │ ├── __init__.py │ └── lfdr.py │ ├── test │ ├── __init__.py │ ├── test_core.py │ ├── test_hail.py │ └── test_pvalues_calculation.py │ └── utils.py ├── scalastyle-config.xml └── src ├── main ├── java │ └── au │ │ └── csiro │ │ ├── sparkle │ │ ├── cmd │ │ │ ├── CmdApp.java │ │ │ ├── DefaultObjectFactory.java │ │ │ └── MultiCmdApp.java │ │ ├── common │ │ │ ├── LoanUtils.java │ │ │ ├── ObjectFactory.java │ │ │ ├── ObjectProvider.java │ │ │ ├── ScalaUtils.java │ │ │ ├── ThrowingConsumer.java │ │ │ ├── ThrowingFunction.java │ │ │ └── args4j │ │ │ │ ├── ArgsApp.java │ │ │ │ ├── ArgsObjectFactory.java │ │ │ │ ├── DateOptionHandler.java │ │ │ │ ├── HasUsage.java │ │ │ │ ├── IntListOptionHandler.java │ │ │ │ ├── ObjectOptionHandler.java │ │ │ │ └── RegisterHandlers.java │ │ └── spark │ │ │ ├── AppContext.java │ │ │ ├── SparkTask.java │ │ │ ├── SparkUtils.java │ │ │ └── SparkleJavaApp.java │ │ └── variantspark │ │ ├── algo │ │ ├── ArrayOps.java │ │ ├── impurity │ │ │ ├── FastGini.java │ │ │ ├── GiniImpurityAggregator.java │ │ │ └── VarianceImpurityAggregator.java │ │ └── split │ │ │ ├── AbstractIndexedSplitterBase.java │ │ │ ├── JNaiveContinousIndexedSplitter.java │ │ │ ├── JOrderedFastIndexedSplitter.java │ │ │ └── JOrderedIndexedSplitter.java │ │ ├── stats │ │ └── CochranArmitageTest.java │ │ └── utils │ │ ├── ArraysUtils.java │ │ ├── FileUtils.java │ │ └── MurMur3Hash.java ├── resources │ └── ref-contigs │ │ └── b37.vcf └── scala │ └── au │ └── csiro │ ├── pbdava │ └── ssparkle │ │ ├── common │ │ ├── arg4j │ │ │ ├── AppRunner.scala │ │ │ ├── AppRunner2.scala │ │ │ └── TestArgs.scala │ │ └── utils │ │ │ ├── CSVUtils.scala │ │ │ ├── FastUtilConversions.scala │ │ │ ├── LoanUtils.scala │ │ │ ├── Logging.scala │ │ │ ├── MiscUtils.scala │ │ │ ├── Prof.scala │ │ │ ├── ReusablePrintStream.scala │ │ │ ├── SerialUtils.scala │ │ │ ├── Timed.scala │ │ │ └── VersionInfo.scala │ │ └── spark │ │ ├── SparkApp.scala │ │ └── SparkUtils.scala │ └── variantspark │ ├── algo │ ├── DecisionTree.scala │ ├── GiniImpurity.scala │ ├── Impurity.scala │ ├── PairwiseOperation.scala │ ├── PredictiveModel.scala │ ├── RandomForest.scala │ ├── Split.scala │ ├── StdTreeFeatures.scala │ ├── TreeFeature.scala │ ├── WideKMeans.scala │ ├── metrics │ │ └── Metrics.scala │ └── package.scala │ ├── api │ ├── AnalyticsFunctions.scala │ ├── CommonPairwiseOperation.scala │ ├── ImportanceAnalysis.scala │ ├── VSContext.scala │ └── package.scala │ ├── cli │ ├── AnalyzeRFCmd.scala │ ├── BuildVarIndexCmd.scala │ ├── CochranArmanCmd.scala │ ├── ConvertCmd.scala │ ├── FilterCmd.scala │ ├── GenerateFeaturesCmd.scala │ ├── GenerateLabelsCmd.scala │ ├── GenerateLabelsNoiseCmd.scala │ ├── ImportanceCmd.scala │ ├── NullImportanceCmd.scala │ ├── PairWiseDistanceCmd.scala │ ├── PredictCmd.scala │ ├── TestCmd.scala │ ├── VariantSparkApp.scala │ ├── VcfToLabels.scala │ ├── VersionCmd.scala │ └── args │ │ ├── FeatureSourceArgs.scala │ │ ├── ImportanceArgs.scala │ │ ├── LabelSourceArgs.scala │ │ ├── ModelOutputArgs.scala │ │ ├── RandomForestArgs.scala │ │ └── SparkArgs.scala │ ├── cmd │ ├── EchoUtils.scala │ └── Echoable.scala │ ├── data │ ├── Data.scala │ ├── Feature.scala │ ├── Representation.scala │ ├── StdData.scala │ ├── VariableType.scala │ └── package.scala │ ├── external │ ├── Model.scala │ └── ModelConverter.scala │ ├── hail │ └── methods │ │ └── RFModel.scala │ ├── input │ ├── CsvFeatureSource.scala │ ├── CsvLabelSource.scala │ ├── CsvStdFeatureSource.scala │ ├── FeatureSource.scala │ ├── HashingLabelSource.scala │ ├── ImputationStrategy.scala │ ├── LabelSource.scala │ ├── ParquetFeatureSource.scala │ ├── VCFFeatureSource.scala │ ├── VCFSource.scala │ └── generate │ │ ├── EffectLabelGenerator.scala │ │ ├── NoisyEffectLabelGenerator.scala │ │ └── OrdinalFeatureGenerator.scala │ ├── metrics │ ├── Gini.scala │ └── Metrics.scala │ ├── output │ ├── CSVFeatureSink.scala │ ├── CSVFeatureSink2.scala │ ├── FeatureSink.scala │ └── ParquetFeatureSink.scala │ ├── python │ └── Metadata.scala │ ├── stats │ └── CochranArmitageTestCalculator.scala │ ├── tests │ ├── TestWideDecisionTree.scala │ └── TestWideKMeans.scala │ ├── utils │ ├── CV.scala │ ├── FactorVariable.scala │ ├── HdfsPath.scala │ ├── Projection.scala │ ├── Sampling.scala │ ├── VectorRDDFunction.scala │ └── package.scala │ └── work │ ├── AnyValTest.scala │ ├── BitsetTest.scala │ ├── BreezeTest.scala │ ├── CaseTest.scala │ ├── DataSetTest.scala │ ├── ImplicitTest.scala │ ├── JSONTest.scala │ ├── ObjectTest.scala │ ├── RandomnesTest.scala │ ├── RegexTest.scala │ ├── StreamTest.scala │ ├── Test.scala │ ├── TestApp.scala │ ├── TestMax.scala │ └── VcfReaderTest.scala └── test ├── R ├── make_stats_case.R ├── make_test_case.R ├── make_test_data.R └── rf_imp_test_case_creator.R ├── data ├── CNAE-9-importance.csv ├── CNAE-9-predicted.csv ├── CNAE-9-tree.csv ├── CNAE-9_R_importance.csv ├── CNAE-9_R_predictions.csv ├── data-importance-stats.csv ├── data-labels.csv ├── data.csv ├── hail │ ├── chr22_1000-22_16050408-pheno.vds │ │ ├── README.txt │ │ ├── _SUCCESS │ │ ├── cols │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0 │ │ ├── entries │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0-2-0-0-f62103ca-78a7-7da5-b23d-9269931965f7 │ │ ├── globals │ │ │ ├── _SUCCESS │ │ │ ├── globals │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ │ └── part-0 │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0 │ │ ├── index │ │ │ └── part-0-2-0-0-f62103ca-78a7-7da5-b23d-9269931965f7.idx │ │ │ │ ├── index │ │ │ │ └── metadata.json.gz │ │ ├── metadata.json.gz │ │ └── rows │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ ├── metadata.json.gz │ │ │ └── parts │ │ │ └── part-0-2-0-0-f62103ca-78a7-7da5-b23d-9269931965f7 │ ├── chr22_1000_missing-22_16050408.vds │ │ ├── README.txt │ │ ├── _SUCCESS │ │ ├── cols │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0 │ │ ├── entries │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0-2-0-0-324e306b-d3e1-b112-3be0-816fdf0278dd │ │ ├── globals │ │ │ ├── _SUCCESS │ │ │ ├── globals │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ │ └── part-0 │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ │ ├── metadata.json.gz │ │ │ │ └── parts │ │ │ │ └── part-0 │ │ ├── index │ │ │ └── part-0-2-0-0-324e306b-d3e1-b112-3be0-816fdf0278dd.idx │ │ │ │ ├── index │ │ │ │ └── metadata.json.gz │ │ ├── metadata.json.gz │ │ └── rows │ │ │ ├── _SUCCESS │ │ │ ├── metadata.json.gz │ │ │ └── rows │ │ │ ├── metadata.json.gz │ │ │ └── parts │ │ │ └── part-0-2-0-0-324e306b-d3e1-b112-3be0-816fdf0278dd │ ├── chr22_22_16050408-imp.csv │ ├── chr22_22_16050408-meta.yml │ └── chr22_22_16050408-model.json ├── regression │ ├── CNAE-9-imp_category.csv │ ├── chr22-imp_22_16050408.csv │ ├── synth_2000_500_fact_10_0.0-imp_cat10.csv │ ├── synth_2000_500_fact_10_0.0-imp_cat2.csv │ ├── synth_2000_500_fact_10_0.995-imp_cat10.csv │ ├── synth_2000_500_fact_10_0.995-imp_cat2.csv │ ├── synth_2000_500_fact_3_0.0-imp_cat10.csv │ ├── synth_2000_500_fact_3_0.0-imp_cat2.csv │ ├── synth_2000_500_fact_3_0.995-imp_cat10.csv │ └── synth_2000_500_fact_3_0.995-imp_cat2.csv ├── simple_ped.ped ├── stats │ ├── stats_100_1000_cont_0.0-labels-stats.csv │ ├── stats_100_1000_cont_0.0-labels.csv │ ├── stats_100_1000_cont_0.0-labels_null-stats.csv │ ├── stats_100_1000_cont_0.0-labels_null.csv │ ├── stats_100_1000_cont_0.0-meta.txt │ ├── stats_100_1000_cont_0.0-std.csv │ └── stats_100_1000_cont_0.0-wide.csv ├── synth │ ├── synth_2000_500_fact_10_0.0-labels.csv │ ├── synth_2000_500_fact_10_0.0-meta.txt │ ├── synth_2000_500_fact_10_0.0-std.csv │ ├── synth_2000_500_fact_10_0.0-wide.csv │ ├── synth_2000_500_fact_10_0.995-labels.csv │ ├── synth_2000_500_fact_10_0.995-meta.txt │ ├── synth_2000_500_fact_10_0.995-std.csv │ ├── synth_2000_500_fact_10_0.995-wide.csv │ ├── synth_2000_500_fact_3_0.0-labels.csv │ ├── synth_2000_500_fact_3_0.0-meta.txt │ ├── synth_2000_500_fact_3_0.0-std.csv │ ├── synth_2000_500_fact_3_0.0-wide.csv │ ├── synth_2000_500_fact_3_0.995-labels.csv │ ├── synth_2000_500_fact_3_0.995-meta.txt │ ├── synth_2000_500_fact_3_0.995-std.csv │ └── synth_2000_500_fact_3_0.995-wide.csv ├── synthetic_100x10k.csv └── synthetic_100x10k_metrics.csv ├── python ├── extract_rf_pheno_vds.py ├── extract_rf_vds.py ├── gen_pw_data.py ├── gen_ranger_dataset.py └── make_test_data.py ├── resources └── log4j.properties └── scala └── au └── csiro └── variantspark ├── algo ├── ArrayOpsTest.scala ├── DecisionTreeNodeTest.scala ├── PairWiseDistanceTest.scala ├── PolymorphicDecisionTreeTest.scala ├── TestPredictorWithImportance.scala ├── TreeDataCollector.scala ├── WideDecisionTreeIntegratedTest.scala ├── WideDecisionTreeModelTest.scala ├── WideRandomForestIntegratedTest.scala ├── WideRandomForrestModelTest.scala ├── WideRandomForrestTest.scala ├── impurity │ └── FastGiniTest.scala ├── metrics │ └── MetricsTest.scala └── split │ └── IndexedSplitterGiniTest.scala ├── api ├── CommonPairwiseOperationTest.scala └── ImportanceApiTest.scala ├── data └── VariableTypeTest.scala ├── external └── ModelConverterTest.scala ├── hail └── methods │ └── RFModelHailTest.scala ├── input ├── CsvStdFeatureSourceTest.scala ├── DefVariantToFeatureConverterTest.scala ├── ModeImputationStrategyTest.scala └── generate │ └── NoisyEffectLabelGeneratorTest.scala ├── metrics ├── GiniTest.scala └── MetricsTest.scala ├── misc └── ReproducibilityTest.scala ├── output └── ParquetFeatureSinkTest.scala ├── perf └── GiniPerfTest.scala ├── python └── MetadataTest.scala ├── test ├── AbstractCmdLineTest.scala ├── SparkTest.scala ├── SparkTestUtils.scala ├── TestCsvUtils.scala ├── TestData.scala ├── TestFeatureSource.scala ├── TestSparkContext.scala ├── regression │ ├── ImportanceDatasetRegressionTest.scala │ ├── ImportanceRegressionTest.scala │ └── ImportanceSynthRegressionTest.scala └── stats │ └── ImportanceStatsTest.scala ├── utils └── 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