LICENSE
README.md
pyproject.toml
setup.py
tests/test_annotator.py
tests/test_checkpoint.py
tests/test_checkpoint_parallel.py
tests/test_checkpoint_parallel_resume.py
tests/test_checkpoint_resume.py
tests/test_chunked_improvements.py
tests/test_chunked_integration.py
tests/test_chunked_vs_nonchunked.py
tests/test_cli.py
tests/test_cli_argument_parsing.py
tests/test_final_filter_simple.py
tests/test_gene_burden.py
tests/test_gene_burden_comprehensive.py
tests/test_gene_burden_integration.py
tests/test_gene_list_annotation.py
tests/test_gene_list_integration.py
tests/test_genotype_utils.py
tests/test_igv_report_generation.py
tests/test_igv_utils.py
tests/test_ped_reader.py
tests/test_pseudonymizer.py
tests/test_sample_column_creation.py
tests/test_scoring_annotated.py
tests/test_scoring_columns.py
tests/test_scoring_inheritance.py
tests/test_scoring_integration.py
tests/test_stats_engine.py
tests/test_stats_integration.py
tests/test_utils.py
variantcentrifuge/__init__.py
variantcentrifuge/_davies_build.py
variantcentrifuge/analysis_profiles.py
variantcentrifuge/analyze_variants.py
variantcentrifuge/annotator.py
variantcentrifuge/build_pm5_lookup.py
variantcentrifuge/checkpoint.py
variantcentrifuge/checkpoint_helpers.py
variantcentrifuge/checkpoint_models.py
variantcentrifuge/checkpoint_state.py
variantcentrifuge/cli.py
variantcentrifuge/cli_analysis_groups.py
variantcentrifuge/cli_config.py
variantcentrifuge/cli_fields.py
variantcentrifuge/cli_memory.py
variantcentrifuge/cli_parser_groups.py
variantcentrifuge/cli_subcommands.py
variantcentrifuge/cli_sync.py
variantcentrifuge/clinvar_pm5.py
variantcentrifuge/config.json
variantcentrifuge/config.py
variantcentrifuge/converter.py
variantcentrifuge/converter_helpers.py
variantcentrifuge/dataframe_optimizer.py
variantcentrifuge/default_stats_config.json
variantcentrifuge/display_utils.py
variantcentrifuge/extractor.py
variantcentrifuge/feature_loaders.py
variantcentrifuge/field_profile.py
variantcentrifuge/filters.py
variantcentrifuge/from_tsv.py
variantcentrifuge/gene_bed.py
variantcentrifuge/gene_burden.py
variantcentrifuge/generate_html_report.py
variantcentrifuge/generate_igv_report.py
variantcentrifuge/genotype_utils.py
variantcentrifuge/gt_reconstruction.py
variantcentrifuge/helpers.py
variantcentrifuge/interactive_resume.py
variantcentrifuge/links.py
variantcentrifuge/ped_reader.py
variantcentrifuge/phenotype.py
variantcentrifuge/phenotype_helpers.py
variantcentrifuge/pipeline.py
variantcentrifuge/pipeline_validation.py
variantcentrifuge/pseudonymizer.py
variantcentrifuge/run_summary.py
variantcentrifuge/sample_sheet.py
variantcentrifuge/scoring.py
variantcentrifuge/scoring_requirements.py
variantcentrifuge/stats.py
variantcentrifuge/stats_engine.py
variantcentrifuge/transcript_filter.py
variantcentrifuge/tsv_filters.py
variantcentrifuge/utils.py
variantcentrifuge/validators.py
variantcentrifuge/vcf_eff_one_per_line.py
variantcentrifuge/vcf_header_parser.py
variantcentrifuge/version.py
variantcentrifuge.egg-info/PKG-INFO
variantcentrifuge.egg-info/SOURCES.txt
variantcentrifuge.egg-info/dependency_links.txt
variantcentrifuge.egg-info/entry_points.txt
variantcentrifuge.egg-info/requires.txt
variantcentrifuge.egg-info/top_level.txt
variantcentrifuge/assets/css/buttons.dataTables.min.css
variantcentrifuge/assets/css/datatables.min.css
variantcentrifuge/assets/css/fixedcolumns.dataTables.min.css
variantcentrifuge/assets/css/nouislider.min.css
variantcentrifuge/assets/css/tippy.css
variantcentrifuge/assets/js/buttons.colVis.min.js
variantcentrifuge/assets/js/chart.umd.min.js
variantcentrifuge/assets/js/chartjs-plugin-datalabels.min.js
variantcentrifuge/assets/js/datatables.buttons.min.js
variantcentrifuge/assets/js/datatables.min.js
variantcentrifuge/assets/js/fixedcolumns.min.js
variantcentrifuge/assets/js/jquery.slim.min.js
variantcentrifuge/assets/js/nouislider.min.js
variantcentrifuge/assets/js/popper.min.js
variantcentrifuge/assets/js/tippy-bundle.umd.min.js
variantcentrifuge/association/__init__.py
variantcentrifuge/association/base.py
variantcentrifuge/association/correction.py
variantcentrifuge/association/covariates.py
variantcentrifuge/association/diagnostics.py
variantcentrifuge/association/engine.py
variantcentrifuge/association/engine_workers.py
variantcentrifuge/association/genotype_matrix.py
variantcentrifuge/association/pca.py
variantcentrifuge/association/weights.py
variantcentrifuge/association/backends/__init__.py
variantcentrifuge/association/backends/base.py
variantcentrifuge/association/backends/coast_python.py
variantcentrifuge/association/backends/davies.py
variantcentrifuge/association/backends/null_model.py
variantcentrifuge/association/backends/python_backend.py
variantcentrifuge/association/backends/r_backend.py
variantcentrifuge/association/backends/skat_math.py
variantcentrifuge/association/backends/skato_integrate.py
variantcentrifuge/association/data/__init__.py
variantcentrifuge/association/data/qfc.cpp
variantcentrifuge/association/meta/__init__.py
variantcentrifuge/association/meta/align.py
variantcentrifuge/association/meta/artifact.py
variantcentrifuge/association/meta/cli.py
variantcentrifuge/association/meta/combine.py
variantcentrifuge/association/meta/heterogeneity.py
variantcentrifuge/association/meta/manifest.py
variantcentrifuge/association/meta/runner.py
variantcentrifuge/association/tests/__init__.py
variantcentrifuge/association/tests/_utils.py
variantcentrifuge/association/tests/acat.py
variantcentrifuge/association/tests/allelic_series.py
variantcentrifuge/association/tests/allelic_series_classify.py
variantcentrifuge/association/tests/allelic_series_python.py
variantcentrifuge/association/tests/allelic_series_r.py
variantcentrifuge/association/tests/fisher.py
variantcentrifuge/association/tests/linear_burden.py
variantcentrifuge/association/tests/logistic_burden.py
variantcentrifuge/association/tests/skat_python.py
variantcentrifuge/association/tests/skat_r.py
variantcentrifuge/inheritance/__init__.py
variantcentrifuge/inheritance/analyzer.py
variantcentrifuge/inheritance/comp_het_vectorized.py
variantcentrifuge/inheritance/deducer.py
variantcentrifuge/inheritance/non_autosomal_deducer.py
variantcentrifuge/inheritance/parallel_analyzer.py
variantcentrifuge/inheritance/prioritizer.py
variantcentrifuge/inheritance/segregation_checker.py
variantcentrifuge/inheritance/vectorized_deducer.py
variantcentrifuge/memory/__init__.py
variantcentrifuge/memory/resource_manager.py
variantcentrifuge/pipeline_core/__init__.py
variantcentrifuge/pipeline_core/context.py
variantcentrifuge/pipeline_core/error_handling.py
variantcentrifuge/pipeline_core/runner.py
variantcentrifuge/pipeline_core/runner_planner.py
variantcentrifuge/pipeline_core/stage.py
variantcentrifuge/pipeline_core/workspace.py
variantcentrifuge/stages/__init__.py
variantcentrifuge/stages/analysis_stage_helpers.py
variantcentrifuge/stages/analysis_stages.py
variantcentrifuge/stages/association_analysis_stages.py
variantcentrifuge/stages/association_outcome.py
variantcentrifuge/stages/bed_stages.py
variantcentrifuge/stages/chunk_helpers.py
variantcentrifuge/stages/chunked_analysis_stages.py
variantcentrifuge/stages/data_loading_stages.py
variantcentrifuge/stages/gene_burden_stages.py
variantcentrifuge/stages/genotype_matrix_builder.py
variantcentrifuge/stages/inheritance_and_scoring_stages.py
variantcentrifuge/stages/metadata_helpers.py
variantcentrifuge/stages/output_stages.py
variantcentrifuge/stages/parallel_processing_stage.py
variantcentrifuge/stages/phenotype_case_control_stages.py
variantcentrifuge/stages/post_processing_stages.py
variantcentrifuge/stages/processing_stages.py
variantcentrifuge/stages/sample_and_pedigree_stages.py
variantcentrifuge/stages/sample_column_helpers.py
variantcentrifuge/stages/setup_stages.py
variantcentrifuge/stages/stage_registry.py
variantcentrifuge/stages/stage_utils.py
variantcentrifuge/stages/statistics_and_clinvar_stages.py
variantcentrifuge/stages/tsv_output_stages.py
variantcentrifuge/stages/variant_analysis_stages.py
variantcentrifuge/templates/index.html