MANIFEST.in
README.md
import.report
pyproject.toml
src/graphmana/__init__.py
src/graphmana/cli.py
src/graphmana/config.py
src/graphmana.egg-info/PKG-INFO
src/graphmana.egg-info/SOURCES.txt
src/graphmana.egg-info/dependency_links.txt
src/graphmana.egg-info/entry_points.txt
src/graphmana.egg-info/requires.txt
src/graphmana.egg-info/top_level.txt
src/graphmana/annotation/__init__.py
src/graphmana/annotation/manager.py
src/graphmana/annotation/parsers/__init__.py
src/graphmana/annotation/parsers/base.py
src/graphmana/annotation/parsers/bed_region.py
src/graphmana/annotation/parsers/cadd.py
src/graphmana/annotation/parsers/clinvar.py
src/graphmana/annotation/parsers/constraint.py
src/graphmana/annotation/parsers/go_pathway.py
src/graphmana/cluster/__init__.py
src/graphmana/cluster/filesystem_check.py
src/graphmana/cluster/neo4j_lifecycle.py
src/graphmana/cohort/__init__.py
src/graphmana/cohort/manager.py
src/graphmana/data/__init__.py
src/graphmana/data/graphmana-procedures.jar
src/graphmana/db/__init__.py
src/graphmana/db/connection.py
src/graphmana/db/queries.py
src/graphmana/db/schema.py
src/graphmana/export/__init__.py
src/graphmana/export/base.py
src/graphmana/export/beagle_export.py
src/graphmana/export/bed_export.py
src/graphmana/export/bgen_export.py
src/graphmana/export/eigenstrat_export.py
src/graphmana/export/gds_export.py
src/graphmana/export/genepop_export.py
src/graphmana/export/hap_export.py
src/graphmana/export/json_export.py
src/graphmana/export/parallel.py
src/graphmana/export/plink2_export.py
src/graphmana/export/plink_export.py
src/graphmana/export/sfs_dadi_export.py
src/graphmana/export/sfs_fsc_export.py
src/graphmana/export/sfs_utils.py
src/graphmana/export/structure_export.py
src/graphmana/export/treemix_export.py
src/graphmana/export/tsv_export.py
src/graphmana/export/vcf_export.py
src/graphmana/export/zarr_export.py
src/graphmana/filtering/__init__.py
src/graphmana/filtering/export_filters.py
src/graphmana/filtering/import_filters.py
src/graphmana/ingest/__init__.py
src/graphmana/ingest/array_ops.py
src/graphmana/ingest/chr_reconciler.py
src/graphmana/ingest/csv_emitter.py
src/graphmana/ingest/genotype_packer.py
src/graphmana/ingest/incremental.py
src/graphmana/ingest/incremental_rebuild.py
src/graphmana/ingest/loader.py
src/graphmana/ingest/normalizer.py
src/graphmana/ingest/parallel.py
src/graphmana/ingest/pipeline.py
src/graphmana/ingest/ploidy_detector.py
src/graphmana/ingest/population_map.py
src/graphmana/ingest/vcf_parser.py
src/graphmana/ingest/vep_parser.py
src/graphmana/liftover/__init__.py
src/graphmana/liftover/chain_parser.py
src/graphmana/liftover/lifter.py
src/graphmana/merge/__init__.py
src/graphmana/merge/merger.py
src/graphmana/migration/__init__.py
src/graphmana/migration/manager.py
src/graphmana/provenance/__init__.py
src/graphmana/provenance/manager.py
src/graphmana/qc/__init__.py
src/graphmana/qc/formatters.py
src/graphmana/qc/manager.py
src/graphmana/qc/ref_check.py
src/graphmana/sample/__init__.py
src/graphmana/sample/manager.py
src/graphmana/snapshot/__init__.py
src/graphmana/snapshot/diff.py
src/graphmana/snapshot/manager.py
tests/__init__.py
tests/conftest.py
tests/test_allele_counting.py
tests/test_annotation_manager.py
tests/test_annotation_queries.py
tests/test_array_ops.py
tests/test_audit_fixes.py
tests/test_base_exporter.py
tests/test_beagle_export.py
tests/test_bed_export.py
tests/test_bed_region_parser.py
tests/test_benchmark_fixtures.py
tests/test_benchmark_measurement.py
tests/test_bgen_export.py
tests/test_cadd_parser.py
tests/test_chr_reconciler.py
tests/test_cli_annotate.py
tests/test_cli_cohort.py
tests/test_cli_diff.py
tests/test_cli_export.py
tests/test_cli_ingest.py
tests/test_cli_parallel.py
tests/test_cli_qc.py
tests/test_cli_sample.py
tests/test_cli_snapshot.py
tests/test_cli_validate.py
tests/test_cli_version.py
tests/test_clinvar_parser.py
tests/test_cluster.py
tests/test_cohort_manager.py
tests/test_connection.py
tests/test_constraint_parser.py
tests/test_csv_emitter.py
tests/test_database_param.py
tests/test_eigenstrat_export.py
tests/test_export_annotation_filters.py
tests/test_export_filters.py
tests/test_export_manifest.py
tests/test_gds_export.py
tests/test_genepop_export.py
tests/test_genotype_packer.py
tests/test_go_pathway_parser.py
tests/test_graphpop_compat.py
tests/test_hap_export.py
tests/test_hard_delete.py
tests/test_import_filters.py
tests/test_incremental.py
tests/test_incremental_rebuild.py
tests/test_json_export.py
tests/test_liftover.py
tests/test_loader.py
tests/test_merge.py
tests/test_migration.py
tests/test_multiallelic.py
tests/test_normalizer.py
tests/test_parallel_export.py
tests/test_parallel_ingest.py
tests/test_pipeline_defaults.py
tests/test_plink2_export.py
tests/test_plink_export.py
tests/test_ploidy_detector.py
tests/test_population_map.py
tests/test_provenance.py
tests/test_provenance_search.py
tests/test_qc_formatters.py
tests/test_qc_manager.py
tests/test_qc_queries.py
tests/test_ref_check.py
tests/test_sample_manager.py
tests/test_sample_queries.py
tests/test_sample_reassign.py
tests/test_schema.py
tests/test_sfs_dadi_export.py
tests/test_sfs_fsc_export.py
tests/test_sfs_utils.py
tests/test_snapshot_manager.py
tests/test_status.py
tests/test_structural_safeguards.py
tests/test_structure_export.py
tests/test_sv_support.py
tests/test_treemix_export.py
tests/test_tsv_export.py
tests/test_vcf_export.py
tests/test_vcf_header.py
tests/test_vep_parser.py
tests/test_zarr_export.py
tests/fixtures/cadd_sample.tsv
tests/fixtures/gnomad_constraint_sample.tsv
tests/fixtures/go_sample.gaf
tests/fixtures/pathway_sample.tsv