├── .dockerignore ├── .editorconfig ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── automerge.yml │ ├── conventional-prs.yml │ ├── deps-report.yml │ ├── docker-build.yml │ ├── docker-cleanup-pr.yml │ ├── docker-cleanup-untagged.yml │ ├── main.yml │ ├── npm-security.yml │ ├── release-please.yml │ └── update-openapi-schema.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yml ├── .release-please-manifest.json ├── CHANGELOG.md ├── CONTRIBUTORS.rst ├── LICENSE ├── Makefile ├── README.md ├── SECURITY.rst ├── VERSION ├── backend ├── .editorconfig ├── .gitattributes ├── .gitignore ├── .protolint.yaml ├── Makefile ├── Pipfile ├── Pipfile.lock ├── beaconsite │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── forms.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20210304_0716.py │ │ ├── 0003_auto_20210304_1052.py │ │ ├── 0004_auto_20210309_1517.py │ │ └── __init__.py │ ├── models.py │ ├── models_api.py │ ├── plugins.py │ ├── rules.py │ ├── templates │ │ └── beaconsite │ │ │ ├── consortium_confirm_delete.html │ │ │ ├── consortium_detail.html │ │ │ ├── consortium_form.html │ │ │ ├── consortium_list.html │ │ │ ├── index.html │ │ │ ├── site_confirm_delete.html │ │ │ ├── site_detail.html │ │ │ ├── site_form.html │ │ │ └── site_list.html │ ├── templatetags │ │ └── __init__.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── test_models.py │ │ ├── test_permissions.py │ │ ├── test_permissions_ajax.py │ │ ├── test_permissions_api.py │ │ ├── test_views.py │ │ ├── test_views_ajax.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ ├── views_ajax.py │ └── views_api.py ├── cases │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20231025_1003.py │ │ ├── 0003_add_fuzzy_stringmatching.py │ │ ├── 0004_userandglobalsettings.py │ │ ├── 0005_auto_20240819_1302.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── rules.py │ ├── serializers.py │ ├── templates │ │ └── cases │ │ │ ├── _details_card.html │ │ │ ├── _search_item.html │ │ │ ├── _search_results.html │ │ │ ├── case │ │ │ ├── indicator_rel_error.html │ │ │ ├── indicator_sex_error.html │ │ │ └── item.html │ │ │ └── entrypoint.html │ ├── templatetags │ │ └── cases_tags.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── snapshots │ │ │ ├── __init__.py │ │ │ └── snap_test_models.py │ │ ├── test_inhouse_db_stats_api.py │ │ ├── test_models.py │ │ ├── test_permissions.py │ │ ├── test_permissions_ajax.py │ │ ├── test_permissions_api.py │ │ ├── test_serializers.py │ │ ├── test_views.py │ │ ├── test_views_ajax.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ ├── views_ajax.py │ └── views_api.py ├── cases_analysis │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models.py │ ├── rules.py │ ├── serializers.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── test_models.py │ │ ├── test_permissions_api.py │ │ └── test_views_api.py │ ├── urls.py │ └── views_api.py ├── cases_files │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20230919_1422.py │ │ ├── 0003_auto_20230926_1324.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py ├── cases_import │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models │ │ ├── __init__.py │ │ ├── base.py │ │ └── executors.py │ ├── plugins.py │ ├── proto.py │ ├── rules.py │ ├── serializers.py │ ├── tasks.py │ ├── templates │ │ └── cases_import │ │ │ ├── _job_view_buttons.html │ │ │ ├── importcasebackgroudjobdetail.html │ │ │ └── index.html │ ├── tests │ │ ├── __init__.py │ │ ├── data │ │ │ ├── family.yaml │ │ │ ├── sample-brca1.vcf.gz │ │ │ ├── sample-brca1.vcf.gz.tbi │ │ │ ├── singleton_cramino_qc.yaml │ │ │ ├── singleton_dragen_qc.yaml │ │ │ ├── singleton_ngsbits_qc.yaml │ │ │ ├── singleton_samtools_qc.yaml │ │ │ ├── singleton_seqvars.yaml │ │ │ └── singleton_strucvars.yaml │ │ ├── factories.py │ │ ├── snapshots │ │ │ ├── __init__.py │ │ │ ├── snap_test_models.py │ │ │ └── snap_test_models_executor.py │ │ ├── test_models.py │ │ ├── test_models_executor.py │ │ ├── test_permissions_api.py │ │ ├── test_proto.py │ │ ├── test_serializers.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ └── views_api.py ├── cases_qc │ ├── __init__.py │ ├── apps.py │ ├── io │ │ ├── __init__.py │ │ ├── cramino.py │ │ ├── dragen.py │ │ ├── ngsbits.py │ │ ├── samtools.py │ │ └── utils.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20240220_1615.py │ │ ├── 0003_auto_20240604_1128.py │ │ └── __init__.py │ ├── models │ │ ├── __init__.py │ │ ├── cramino.py │ │ ├── dragen.py │ │ ├── ngsbits.py │ │ ├── samtools.py │ │ └── varfish.py │ ├── rules.py │ ├── serializers.py │ ├── tasks.py │ ├── tests │ │ ├── __init__.py │ │ ├── data │ │ │ ├── sample.bcftools-stats.txt │ │ │ ├── sample.cnv_metrics.csv │ │ │ ├── sample.cramino.txt │ │ │ ├── sample.fragment_length_hist.csv │ │ │ ├── sample.gvcf_hethom_ratio_metrics.csv │ │ │ ├── sample.gvcf_metrics.csv │ │ │ ├── sample.mapping_metrics.csv │ │ │ ├── sample.ngsbits-mappingqc.txt │ │ │ ├── sample.ploidy_estimation_metrics.csv │ │ │ ├── sample.qc-coverage-region-1_contig_mean_cov.csv │ │ │ ├── sample.qc-coverage-region-1_coverage_metrics.csv │ │ │ ├── sample.qc-coverage-region-1_fine_hist.csv │ │ │ ├── sample.qc-coverage-region-1_hist.csv │ │ │ ├── sample.qc-coverage-region-1_overall_mean_cov.csv │ │ │ ├── sample.qc-coverage-region-2_contig_mean_cov.csv │ │ │ ├── sample.qc-coverage-region-2_coverage_metrics.csv │ │ │ ├── sample.qc-coverage-region-2_fine_hist.csv │ │ │ ├── sample.qc-coverage-region-2_hist.csv │ │ │ ├── sample.qc-coverage-region-2_overall_mean_cov.csv │ │ │ ├── sample.qc-coverage-region-3_contig_mean_cov.csv │ │ │ ├── sample.qc-coverage-region-3_coverage_metrics.csv │ │ │ ├── sample.qc-coverage-region-3_fine_hist.csv │ │ │ ├── sample.qc-coverage-region-3_hist.csv │ │ │ ├── sample.qc-coverage-region-3_overall_mean_cov.csv │ │ │ ├── sample.roh_metrics.csv │ │ │ ├── sample.samtools-flagstat.txt │ │ │ ├── sample.samtools-idxstats.txt │ │ │ ├── sample.samtools-stats.txt │ │ │ ├── sample.sv_metrics.csv │ │ │ ├── sample.time_metrics.csv │ │ │ ├── sample.trimmer_metrics.csv │ │ │ ├── sample.vc_hethom_ratio_metrics.csv │ │ │ ├── sample.vc_metrics.csv │ │ │ ├── sample.wgs_contig_mean_cov.csv │ │ │ ├── sample.wgs_coverage_metrics.csv │ │ │ ├── sample.wgs_fine_hist.csv │ │ │ ├── sample.wgs_hist.csv │ │ │ └── sample.wgs_overall_mean_cov.csv │ │ ├── factories.py │ │ ├── helpers.py │ │ ├── snapshots │ │ │ ├── __init__.py │ │ │ ├── snap_test_io_cramino.py │ │ │ ├── snap_test_io_dragen.py │ │ │ ├── snap_test_io_ngsbits.py │ │ │ ├── snap_test_io_samtools.py │ │ │ ├── snap_test_serializers.py │ │ │ └── snap_test_views_api.py │ │ ├── test_io_cramino.py │ │ ├── test_io_dragen.py │ │ ├── test_io_ngsbits.py │ │ ├── test_io_samtools.py │ │ ├── test_models.py │ │ ├── test_permissions_api.py │ │ ├── test_serializers.py │ │ └── test_views_api.py │ ├── urls.py │ └── views_api.py ├── clinvar │ ├── __init__.py │ ├── apps.py │ ├── clinvar_models.py │ ├── management │ │ └── commands │ │ │ └── import_clinvar_jsonl.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_clinvarpathogenicgenes.py │ │ ├── 0003_auto_20190619_1636.py │ │ ├── 0004_delete_clinvar.py │ │ ├── 0005_auto_20200611_1719.py │ │ ├── 0006_clinvarpathogenicgenes.py │ │ ├── 0007_alter_clinvar_details.py │ │ ├── 0008_auto_20220829_1132.py │ │ ├── 0009_auto_20220908_1430.py │ │ ├── 0010_clinvarpathogenicgenes.py │ │ └── __init__.py │ ├── models.py │ ├── templatetags │ │ ├── __init__.py │ │ └── clinvar_tags.py │ └── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py ├── clinvar_export │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_bootstrap_records.py │ │ ├── 0003_auto_20211129_1443.py │ │ ├── 0004_auto_20221028_0657.py │ │ ├── 0005_auto_20240603_1606.py │ │ └── __init__.py │ └── plugins.py ├── cohorts │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_cohort_name.py │ │ ├── 0003_auto_20200701_1255.py │ │ ├── 0004_auto_20200710_1548.py │ │ ├── 0005_auto_20230102_1310.py │ │ ├── 0006_auto_20230102_1310.py │ │ ├── 0007_alter_cohort_cases.py │ │ ├── 0008_alter_cohort_user.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── rules.py │ ├── serializers.py │ ├── templates │ │ └── cohorts │ │ │ └── entrypoint.html │ ├── tests │ │ ├── factories.py │ │ ├── test_models.py │ │ ├── test_permissions_ajax.py │ │ ├── test_permissions_api.py │ │ ├── test_views_ajax.py │ │ ├── test_views_api.py │ │ └── test_views_ui.py │ ├── urls.py │ ├── views.py │ ├── views_ajax.py │ └── views_api.py ├── config │ ├── __init__.py │ ├── celery.py │ ├── common.py │ ├── settings │ │ ├── __init__.py │ │ ├── base.py │ │ ├── local.py │ │ ├── production.py │ │ └── test.py │ ├── urls.py │ └── wsgi.py ├── conservation │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190619_0926.py │ │ ├── 0003_knowngeneaa_bin.py │ │ ├── 0004_auto_20200106_1000.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ └── factories.py ├── dbsnp │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190619_1636.py │ │ ├── 0003_auto_20190705_1321.py │ │ ├── 0004_int_to_bigint.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ └── factories.py ├── dot_env.example ├── env.example ├── ext_gestaltmatcher │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_smallvariantquerypediascores.py │ │ ├── 0003_auto_20241009_0639.py │ │ └── __init__.py │ └── models.py ├── extra_annos │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20200714_1411.py │ │ ├── 0003_alter_extraanno_anno_data.py │ │ ├── 0004_alter_extraanno_anno_data.py │ │ ├── 0005_int_to_bigint.py │ │ └── __init__.py │ ├── models.py │ ├── tests │ │ ├── __init__.py │ │ └── factories.py │ └── views.py ├── frequencies │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190619_1636.py │ │ ├── 0003_auto_20190705_1321.py │ │ ├── 0004_auto_20191107_1047.py │ │ ├── 0005_auto_20200123_1033.py │ │ ├── 0006_remove_mtdb_gap.py │ │ ├── 0007_auto_20200211_1625.py │ │ ├── 0008_alter_mtdb_synonymous.py │ │ ├── 0009_auto_20220830_0622.py │ │ └── __init__.py │ ├── models.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py │ └── views.py ├── geneinfo │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20181106_1022.py │ │ ├── 0003_auto_20181127_1320.py │ │ ├── 0004_auto_20181204_1027.py │ │ ├── 0005_auto_20190104_1554.py │ │ ├── 0006_auto_20190319_1638.py │ │ ├── 0007_refseqtohgnc.py │ │ ├── 0008_acmg.py │ │ ├── 0009_auto_20190426_0704.py │ │ ├── 0010_exacconstraints_gnomadconstraints.py │ │ ├── 0011_ensembltorefseq.py │ │ ├── 0012_refseqtoensembl.py │ │ ├── 0013_materialized_view_geneidtoinheritance.py │ │ ├── 0014_mgihommousehumansequence.py │ │ ├── 0015_mgimapping.py │ │ ├── 0016_mgimapping_index.py │ │ ├── 0017_auto_20191004_1414.py │ │ ├── 0018_auto_20191014_1218.py │ │ ├── 0019_ncbigenerif_pubmed_ids.py │ │ ├── 0020_auto_20191118_1729.py │ │ ├── 0021_auto_20200106_1000.py │ │ ├── 0022_materialized_view_geneidinhpo.py │ │ ├── 0023_materialized_view_geneidinhpo_fix.py │ │ ├── 0024_alter_ncbigenerif_pubmed_ids.py │ │ ├── 0025_auto_20211019_0829.py │ │ ├── 0026_hgnc_gtrnadb.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py ├── genepanels │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── forms.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── rules.py │ ├── serializers.py │ ├── templates │ │ └── genepanels │ │ │ ├── _project_menu_btn.html │ │ │ ├── category_confirm_delete.html │ │ │ ├── category_detail.html │ │ │ ├── category_form.html │ │ │ ├── category_list.html │ │ │ ├── genepanel_confirm.html │ │ │ ├── genepanel_detail.html │ │ │ ├── genepanel_form.html │ │ │ └── index.html │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── test_forms.py │ │ ├── test_models.py │ │ ├── test_permissions.py │ │ └── test_views.py │ ├── urls.py │ ├── views.py │ └── views_api.py ├── genomicfeatures │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190523_1346.py │ │ ├── 0003_auto_20190619_1529.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py ├── hgmd │ ├── __init__.py │ ├── apps.py │ └── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190425_1523.py │ │ ├── 0003_hgmdpubliclocus_bin.py │ │ ├── 0004_auto_20190830_1126.py │ │ ├── 0005_delete_hgmdpubliclocus.py │ │ └── __init__.py ├── importer │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── management │ │ ├── commands │ │ │ ├── import_case.py │ │ │ ├── import_cases_bulk.py │ │ │ ├── import_tables.py │ │ │ ├── pg_dump.py │ │ │ ├── rebuild_project_case_stats.py │ │ │ ├── rebuild_project_stats.py │ │ │ └── rebuild_variant_summary.py │ │ └── helpers.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190215_1744.py │ │ ├── 0003_auto_20190409_1101.py │ │ ├── 0004_auto_20190415_0912.py │ │ ├── 0005_auto_20200129_1600.py │ │ ├── 0006_auto_20200130_1538.py │ │ ├── 0007_auto_20200203_1242.py │ │ ├── 0008_variantsetimportinfo_state.py │ │ ├── 0009_alter_caseimportinfo_pedigree.py │ │ ├── 0010_auto_20220112_0657.py │ │ ├── 0011_casegeneannotationfile.py │ │ ├── 0012_alter_importcasebgjob_bg_job.py │ │ ├── 0013_alter_caseimportinfo_status.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── qc_schemas.py │ ├── rules.py │ ├── schemas │ │ ├── case-qc-v1.json │ │ └── examples │ │ │ └── trio.json │ ├── serializers.py │ ├── tasks.py │ ├── templates │ │ └── importer │ │ │ ├── import_case_detail.html │ │ │ └── importinfo.html │ ├── tests │ │ ├── __init__.py │ │ ├── data │ │ │ └── example.tsv │ │ ├── factories.py │ │ ├── test_schemas.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ └── views_api.py ├── maintenance │ ├── __init__.py │ ├── apps.py │ └── management │ │ ├── __init__.py │ │ └── commands │ │ ├── __init__.py │ │ ├── check_installation.py │ │ ├── clear_expired_files.py │ │ ├── clear_inactive_variant_sets.py │ │ ├── clear_old_kiosk_cases.py │ │ ├── copy_presets.py │ │ ├── generate_result_set.py │ │ ├── remove_invalid_queries.py │ │ ├── repair_result_set.py │ │ └── transfer_presets.py ├── manage.py ├── misc │ ├── big-starfish-svgrepo-com-bw.svg │ ├── big-starfish-svgrepo-com-bw.svg.png │ ├── big-starfish-svgrepo-com.svg │ ├── favicon-32x32.png │ └── nltk_data │ │ ├── corpora │ │ └── stopwords │ │ │ └── english │ │ └── tokenizers │ │ └── punkt │ │ ├── PY3 │ │ └── english.pickle │ │ └── english.pickle ├── pathways │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models.py │ └── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py ├── protos │ └── seqvars │ │ └── protos │ │ ├── output.proto │ │ └── query.proto ├── pyproject.toml ├── regmaps │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── cmds.py │ ├── management │ │ └── commands │ │ │ ├── regmap_delete.py │ │ │ ├── regmap_import.py │ │ │ └── regmap_list.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20211008_1015.py │ │ └── __init__.py │ ├── models.py │ ├── templatetags │ │ ├── __init__.py │ │ └── regmaps_tags.py │ └── tests │ │ ├── __init__.py │ │ ├── ex_coll │ │ ├── MA │ │ │ ├── elements.bed │ │ │ └── interactions.bed │ │ ├── README.md │ │ └── index.yml │ │ ├── factories.py │ │ ├── test_cmds.py │ │ └── test_models.py ├── seqmeta │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_alter_targetbedfile_file_uri.py │ │ ├── 0003_targetbedfile_seqmeta_tar_file_ur_9f92c4_idx.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── rules.py │ ├── serializers.py │ ├── templates │ │ └── seqmeta │ │ │ ├── _project_menu_btn.html │ │ │ ├── enrichmentkit_detail.html │ │ │ ├── enrichmentkit_list.html │ │ │ └── index.html │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── test_models.py │ │ ├── test_permissions.py │ │ ├── test_permissions_api.py │ │ ├── test_views.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ └── views_api.py ├── seqvars │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── factory_defaults.py │ ├── management │ │ └── commands │ │ │ ├── buildseqvarsinhousedb.py │ │ │ ├── runseqvarsquery.py │ │ │ └── runtask.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20240708_1305.py │ │ ├── 0003_seqvarsquerysettings_predefinedquery.py │ │ ├── 0004_auto_20240712_1236.py │ │ ├── 0005_seqvarsquerysettingsgenotype_recessive_mode.py │ │ ├── 0006_auto_20240807_1006.py │ │ ├── 0007_auto_20240822_1314.py │ │ ├── 0008_seqvarsqueryexecutionbackgroundjob.py │ │ ├── 0009_alter_seqvarsresultrow_genome_release.py │ │ ├── 0010_auto_20240905_1017.py │ │ ├── 0011_alter_seqvarsqueryexecution_options.py │ │ ├── 0012_auto_20241024_0823.py │ │ ├── 0013_auto_20241028_0928.py │ │ ├── 0014_seqvarsquerypresetsset_is_factory_default.py │ │ ├── 0015_seqvarsinhousedbbuildbackgroundjob.py │ │ └── __init__.py │ ├── models │ │ ├── __init__.py │ │ ├── base.py │ │ ├── executors.py │ │ └── protobufs.py │ ├── plugins.py │ ├── protos │ │ ├── __init__.py │ │ ├── output_pb2.py │ │ ├── output_pb2.pyi │ │ ├── query_pb2.py │ │ └── query_pb2.pyi │ ├── rules.py │ ├── serializers.py │ ├── tasks.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── snapshots │ │ │ ├── __init__.py │ │ │ ├── snap_test_factory_defaults.py │ │ │ └── snap_test_models.py │ │ ├── test_factory_defaults.py │ │ ├── test_models.py │ │ ├── test_permissions_api.py │ │ ├── test_serializers.py │ │ └── test_views_api.py │ ├── urls.py │ └── views_api.py ├── setup.cfg ├── svdbs │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_auto_20190619_1529.py │ │ ├── 0003_auto_20190723_0934.py │ │ ├── 0004_auto_20210617_1409.py │ │ └── __init__.py │ ├── models.py │ ├── templatetags │ │ ├── __init__.py │ │ └── svdbs_tags.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ └── test_models.py │ └── views.py ├── svs │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── bg_db.py │ ├── forms.py │ ├── management │ │ └── commands │ │ │ ├── svs_bg_sv_set_build.py │ │ │ ├── svs_bg_sv_set_cleanup.py │ │ │ ├── svs_bg_sv_set_dump.py │ │ │ ├── svs_bg_sv_set_list.py │ │ │ ├── svs_sv_fill_nulls.py │ │ │ └── svs_svs_dump.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_pgplsql_overlapping_bins.py │ │ ├── 0003_auto_20190619_1529.py │ │ ├── 0004_auto_20190702_0625.py │ │ ├── 0005_importstructuralvariantbgjob.py │ │ ├── 0006_auto_20190703_1709.py │ │ ├── 0007_partition_sv_tables.py │ │ ├── 0008_set_unlogged_table.py │ │ ├── 0009_auto_20191017_0853.py │ │ ├── 0010_set_logged_table.py │ │ ├── 0011_rename_partitions.py │ │ ├── 0012_structuralvariantflags_flag_molecular.py │ │ ├── 0013_auto_20200909_1401.py │ │ ├── 0014_svs_stucturalvariants_alter_unique_constraint.py │ │ ├── 0015_set_logged_table.py │ │ ├── 0016_structuralvariantset_release.py │ │ ├── 0017_backgroundsv_backgroundsvset_buildbackgroundsvsetjob_cleanupbackgroundsvsetjob.py │ │ ├── 0018_extend_structuralvariant.py │ │ ├── 0019_backgroundsv_svs_backgro_bg_sv_s_72b34f_idx.py │ │ ├── 0020_filtersvbgjob_svquery_svqueryresultrow_svqueryresultset.py │ │ ├── 0021_remove_svqueryresultset_query_sql.py │ │ ├── 0022_auto_20230801_1417.py │ │ ├── 0023_int_to_bigint.py │ │ ├── 0024_clear_sv_queries.py │ │ ├── 0025_structuralvariantflags_flag_incidental.py │ │ ├── 0026_auto_20240522_1353.py │ │ ├── 0027_auto_20240529_1403.py │ │ ├── 0028_auto_20240807_0850.py │ │ ├── 0029_alter_buildbackgroundsvsetjob_bg_job_and_more.py │ │ └── __init__.py │ ├── models │ │ ├── __init__.py │ │ ├── bg_db.py │ │ ├── importer.py │ │ ├── jobs.py │ │ ├── queries.py │ │ ├── records.py │ │ └── user_annos.py │ ├── plugins.py │ ├── query_presets.py │ ├── query_schemas.py │ ├── rules.py │ ├── serializers │ │ ├── __init__.py │ │ ├── presets.py │ │ ├── queries.py │ │ └── user_annos.py │ ├── tasks.py │ ├── templates │ │ └── svs │ │ │ ├── build_bg_job_detail.html │ │ │ ├── cleanup_bg_job_detail.html │ │ │ ├── entrypoint.html │ │ │ └── import_job_detail.html │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── helpers.py │ │ ├── snapshots │ │ │ ├── __init__.py │ │ │ └── snap_test_query_presets.py │ │ ├── test_bg_db.py │ │ ├── test_import.py │ │ ├── test_models.py │ │ ├── test_models_jobs.py │ │ ├── test_permissions_ajax_presets.py │ │ ├── test_permissions_ajax_queries.py │ │ ├── test_query_presets.py │ │ ├── test_serializers.py │ │ ├── test_views.py │ │ ├── test_views_ajax_queries.py │ │ └── test_views_ajax_user_annos.py │ ├── urls.py │ └── views │ │ ├── __init__.py │ │ ├── ajax │ │ ├── __init__.py │ │ ├── details.py │ │ ├── presets.py │ │ ├── queries.py │ │ ├── user_annos.py │ │ └── variants.py │ │ └── bgjob.py ├── templatetags │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ └── __init__.py │ └── templatetags │ │ ├── __init__.py │ │ ├── dict.py │ │ └── json.py ├── var_stats_qc │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── data │ │ ├── grch37_sites.tsv │ │ └── grch38_sites.tsv │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_import_grch37_sites.py │ │ ├── 0003_auto_20190619_1636.py │ │ ├── 0004_auto_20190628_0735.py │ │ ├── 0005_import_grch38_sites.py │ │ └── __init__.py │ ├── models.py │ ├── qc.py │ └── tests.py ├── varannos │ ├── __init__.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models.py │ ├── plugins.py │ ├── queries.py │ ├── rules.py │ ├── serializers.py │ ├── templates │ │ └── varannos │ │ │ ├── _details_card.html │ │ │ ├── varannoset │ │ │ └── item.html │ │ │ ├── varannoset_detail.html │ │ │ └── varannoset_list.html │ ├── templatetags │ │ ├── __init__.py │ │ └── varannos_tags.py │ ├── tests │ │ ├── __init__.py │ │ ├── factories.py │ │ ├── helpers.py │ │ ├── test_models.py │ │ ├── test_permissions.py │ │ ├── test_permissions_api.py │ │ ├── test_plugins.py │ │ ├── test_queries.py │ │ ├── test_varanno_tags.py │ │ ├── test_views.py │ │ └── test_views_api.py │ ├── urls.py │ ├── views.py │ └── views_api.py ├── varfish │ ├── __init__.py │ ├── api_utils.py │ ├── contrib │ │ ├── __init__.py │ │ └── sites │ │ │ ├── __init__.py │ │ │ └── migrations │ │ │ ├── 0001_initial.py │ │ │ ├── 0002_alter_domain_unique.py │ │ │ ├── 0003_set_site_domain_and_name.py │ │ │ ├── 0004_alter_site_options.py │ │ │ └── __init__.py │ ├── media │ │ └── importer │ │ │ ├── 2ec18731-48c4-4cc6-9984-dfdc8707e610 │ │ │ └── genotype_file │ │ │ │ └── 16eff5eb-821c-4152-9809-5f0c6219da79 │ │ │ ├── 57330657-b229-4f86-806e-12243fa921cd │ │ │ └── bam_qc_file │ │ │ │ └── a961fd4e-1bd9-4e60-93a8-64031636a85b │ │ │ ├── 7e5444a8-58e8-4de9-afee-6b9605672a5c │ │ │ └── bam_qc_file │ │ │ │ └── ab8af3eb-8c3b-405c-8067-772434f1d39c │ │ │ ├── 95f9a0c5-2df4-4cd3-8ef3-e7519bc1b827 │ │ │ └── genotype_file │ │ │ │ └── c86480b3-0317-4ac6-8899-4bdd4e0c00d2 │ │ │ ├── d71504bf-ea56-4670-abda-6a8b25ee33f0 │ │ │ └── genotype_file │ │ │ │ ├── 22cb11f0-b847-4da6-915e-38d1126e1264 │ │ │ │ └── b7c83459-6cdb-40ab-a7e8-2e1be581087d │ │ │ └── f39ebc64-0433-4017-b5fb-19057db2822c │ │ │ └── bam_qc_file │ │ │ ├── 8ffb80c6-9810-4a5b-b308-22d5ceef83c1 │ │ │ └── 93d3db15-5d0b-4f3a-a6c3-fda5b8f1be01 │ ├── spectacular_utils.py │ ├── static │ │ ├── .dockerignore │ │ ├── .gitignore │ │ ├── css │ │ │ ├── images │ │ │ │ ├── sort_asc.png │ │ │ │ ├── sort_asc_disabled.png │ │ │ │ ├── sort_both.png │ │ │ │ ├── sort_desc.png │ │ │ │ └── sort_desc_disabled.png │ │ │ └── project.css │ │ ├── fonts │ │ │ └── .gitkeep │ │ ├── images │ │ │ ├── favicon │ │ │ │ └── favicon-32x32.png │ │ │ └── logo_navbar.png │ │ ├── js │ │ │ └── project.js │ │ └── sass │ │ │ ├── custom_bootstrap_vars.scss │ │ │ └── project.scss │ ├── templates │ │ ├── 403_csrf.html │ │ ├── 404.html │ │ ├── 500.html │ │ ├── base.html │ │ ├── bootstrap4 │ │ │ ├── field.html │ │ │ └── layout │ │ │ │ └── field_errors_block.html │ │ ├── empty_base.html │ │ ├── include │ │ │ ├── _footer.html │ │ │ └── _titlebar_nav.html │ │ ├── pages │ │ │ ├── about.html │ │ │ └── home.html │ │ └── users │ │ │ └── login.html │ ├── tests │ │ └── drf_openapi_schema │ │ │ ├── README │ │ │ └── varfish_api_schema.yaml │ ├── users │ │ ├── __init__.py │ │ ├── adapters.py │ │ ├── admin.py │ │ ├── apps.py │ │ ├── management │ │ │ └── commands │ │ │ │ ├── data │ │ │ │ ├── Case_1.grch37.delly2.vcf.gz │ │ │ │ ├── Case_1.grch37.delly2.vcf.gz.tbi │ │ │ │ ├── Case_1.grch37.gatk_hc.vcf.gz │ │ │ │ ├── Case_1.grch37.gatk_hc.vcf.gz.tbi │ │ │ │ ├── Case_1.grch37.yaml.tpl │ │ │ │ ├── Case_1.ped │ │ │ │ ├── Case_1_exons.grch37.delly2.vcf.gz │ │ │ │ ├── Case_1_exons.grch37.delly2.vcf.gz.tbi │ │ │ │ ├── Case_1_exons.grch37.gatk_hc.vcf.gz │ │ │ │ ├── Case_1_exons.grch37.gatk_hc.vcf.gz.tbi │ │ │ │ ├── Case_1_exons.grch37.yaml.tpl │ │ │ │ └── Case_1_exons.ped │ │ │ │ └── initdev.py │ │ ├── migrations │ │ │ ├── 0001_initial.py │ │ │ ├── 0002_auto_20181015_1316.py │ │ │ ├── 0003_auto_20200505_0724.py │ │ │ ├── 0004_auto_20210617_1409.py │ │ │ └── __init__.py │ │ ├── models.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── factories.py │ │ │ ├── test_admin.py │ │ │ └── test_models.py │ │ ├── urls.py │ │ └── views.py │ ├── utils.py │ └── vueapp │ │ ├── __init__.py │ │ ├── apps.py │ │ ├── plugins.py │ │ ├── templatetags │ │ ├── __init__.py │ │ └── vite_tags.py │ │ ├── urls.py │ │ └── views_ajax.py └── variants │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── file_export.py │ ├── forms.py │ ├── helpers.py │ ├── migrations │ ├── 0001_initial.py │ ├── 0002_exportfilebgjob_exportfilejobresult.py │ ├── 0003_auto_20181031_1531.py │ ├── 0004_auto_20181031_1607.py │ ├── 0005_load_btree_gin_extension.py │ ├── 0006_auto_20181106_1022.py │ ├── 0007_auto_20181108_1122.py │ ├── 0008_auto_20181113_1912.py │ ├── 0009_smallvariantcomment.py │ ├── 0010_add_has_gt_entries_to_pedigree.py │ ├── 0011_case_search_tokens.py │ ├── 0012_auto_20181114_1914.py │ ├── 0013_smallvariantflags_flag_summary.py │ ├── 0014_auto_20181115_1426.py │ ├── 0015_auto_20181116_1437.py │ ├── 0016_smallvariantquery.py │ ├── 0017_distillersubmissionbgjob.py │ ├── 0018_casevariantstats_pedigreerelatedness_samplevariantstatistics.py │ ├── 0019_rebuild_var_stats.py │ ├── 0020_auto_20181126_1930.py │ ├── 0021_auto_20181127_0911.py │ ├── 0022_auto_20181127_1110.py │ ├── 0023_auto_20181127_1315.py │ ├── 0024_auto_20181130_0822.py │ ├── 0025_smallvariant_bigint_id_field.py │ ├── 0026_auto_20190128_1210.py │ ├── 0027_filter_jobs_bigint_id_field.py │ ├── 0028_auto_20190219_0738.py │ ├── 0029_auto_20190306_0727.py │ ├── 0030_auto_20190307_0723.py │ ├── 0031_smallvariantquerygenescores.py │ ├── 0032_auto_20190320_2042.py │ ├── 0033_smallvariantsummary.py │ ├── 0034_smallvariantqueryvariantscores.py │ ├── 0035_auto_20190403_0911.py │ ├── 0036_auto_20190412_1113.py │ ├── 0037_auto_20190415_0921.py │ ├── 0038_auto_20190507_1155.py │ ├── 0039_acmgcriteriarating.py │ ├── 0040_case_variant_counts.py │ ├── 0041_array_cat_agg.py │ ├── 0042_auto_20190619_1636.py │ ├── 0043_synccaselistbgjob_synccaseresultmessage.py │ ├── 0044_adjust_smallvariantstats.py │ ├── 0045_auto_20190628_1233.py │ ├── 0046_partition_smallvariants_table.py │ ├── 0047_auto_20190701_1625.py │ ├── 0048_importvariantsbgjob.py │ ├── 0049_auto_20190703_1316.py │ ├── 0050_auto_20190731_1109.py │ ├── 0051_case_notes.py │ ├── 0052_case_status.py │ ├── 0053_auto_20190809_1636.py │ ├── 0054_set_unlogged_table.py │ ├── 0055_auto_20190828_1408.py │ ├── 0056_add_info_and_distance.py │ ├── 0057_auto_20190920_0801.py │ ├── 0058_auto_20190923_1548.py │ ├── 0059_smallvariantqueryvariantscores_api_result.py │ ├── 0060_auto_20191004_1414.py │ ├── 0061_auto_20191017_0729.py │ ├── 0062_auto_20191018_0906.py │ ├── 0063_auto_20191022_1232.py │ ├── 0064_auto_20191025_1403.py │ ├── 0065_projectcasessmallvariantqueryvariantscores.py │ ├── 0066_case_tags.py │ ├── 0067_smallvariant_seq_id_bigint.py │ ├── 0068_kioskannotatebgjob.py │ ├── 0069_set_logged_table.py │ ├── 0070_smallvariant_create_index_chromosome_no.py │ ├── 0071_smallvariantflags_flag_molecular.py │ ├── 0072_deletecasebgjob.py │ ├── 0073_clearexpiredexportedfilesbgjob_clearinactivevariantsetsbgjob_clearoldkioskcasesbgjob_refreshsmallvar.py │ ├── 0074_caddsubmissionbgjob.py │ ├── 0075_projectcasesfilterbgjob_cohort.py │ ├── 0076_auto_20200727_1558.py │ ├── 0077_set_latest_variant_sets.py │ ├── 0078_exportprojectcasesfilebgjob_cohort.py │ ├── 0079_auto_20210204_1006.py │ ├── 0080_spanrsubmissionbgjob.py │ ├── 0081_set_logged_table_again.py │ ├── 0082_auto_20210617_1409.py │ ├── 0083_auto_20211129_1443.py │ ├── 0084_auto_20220112_0657.py │ ├── 0085_add_variant_index.py │ ├── 0086_smallvariantsummary_excludefrominhousedb.py │ ├── 0087_casegeneannotationentry.py │ ├── 0088_auto_20221104_1450.py │ ├── 0089_auto_20221109_1426.py │ ├── 0090_populate_uuids.py │ ├── 0091_alter_casephenotypeterms_sodar_uuid.py │ ├── 0092_auto_20230703_1041.py │ ├── 0093_auto_20230711_1501.py │ ├── 0094_auto_20230719_1406.py │ ├── 0095_auto_20230724_0820.py │ ├── 0096_impactpresets_max_exon_dist.py │ ├── 0097_int_to_bigint.py │ ├── 0098_alter_acmgcriteriarating_options.py │ ├── 0099_auto_20240301_1141_nullable_sodar_uuid.py │ ├── 0100_auto_20240301_1141_fill_sodar_uuid.py │ ├── 0101_auto_20240301_1141_not_null_sodar_field.py │ ├── 0102_auto_20240322_1502.py │ ├── 0103_presetset_default_presetset.py │ ├── 0104_remove_hgmd_dbsnp_filter_from_query_settings.py │ ├── 0105_auto_20240529_1403.py │ ├── 0106_quickpresets_position.py │ ├── 0107_alter_quickpresets_options.py │ ├── 0108_auto_20240807_0850.py │ ├── 0109_alter_clearexpiredexportedfilesbgjob_bg_job_and_more.py │ ├── 0110_drop_variant_summary.py │ ├── 0111_create_variant_summary.py │ ├── 0112_alter_case_status.py │ └── __init__.py │ ├── models │ ├── __init__.py │ ├── case.py │ ├── export.py │ ├── extsub.py │ ├── importer.py │ ├── jobs.py │ ├── kiosk.py │ ├── maintenance.py │ ├── presets.py │ ├── projectroles.py │ ├── queries.py │ ├── scores.py │ ├── stats.py │ ├── summary.py │ ├── userannos.py │ └── variants.py │ ├── plugins.py │ ├── queries.py │ ├── query_presets.py │ ├── query_schemas.py │ ├── rules.py │ ├── schemas │ ├── case-query-v1.json │ └── examples │ │ ├── case-query-v1-01-minimal-with-defaults.json │ │ ├── case-query-v1-01-minimal.json │ │ ├── case-query-v1-02-singleton-with-defaults.json │ │ └── case-query-v1-02-singleton.json │ ├── serializers │ ├── __init__.py │ ├── case.py │ └── presets.py │ ├── submit_external.py │ ├── submit_filter.py │ ├── sync_upstream.py │ ├── tasks.py │ ├── templates │ └── variants │ │ ├── _details_card.html │ │ ├── _job_view_buttons.html │ │ ├── background_job_list.html │ │ ├── cadd_job_detail.html │ │ ├── case_delete_job_detail.html │ │ ├── distiller_job_detail.html │ │ ├── entrypoint.html │ │ ├── export_job_detail.html │ │ ├── export_project_cases_job_detail.html │ │ ├── filter_job_detail.html │ │ ├── import_job_detail.html │ │ ├── maintenance_job_detail.html │ │ ├── project_stats_job_detail.html │ │ ├── spanr_job_detail.html │ │ └── sync_job_detail.html │ ├── templatetags │ ├── __init__.py │ └── variants_tags.py │ ├── tests │ ├── __init__.py │ ├── _fixtures.py │ ├── data │ │ ├── isa_tab_singleton │ │ │ ├── a_varfish_test_singleton_exome_sequencing_nucleotide_sequencing.txt │ │ │ ├── i_Investigation.txt │ │ │ └── s_varfish_test_singleton.txt │ │ └── query_settings.py │ ├── factories.py │ ├── helpers.py │ ├── test_file_export.py │ ├── test_import.py │ ├── test_models.py │ ├── test_models_presets.py │ ├── test_permissions_ajax.py │ ├── test_permissions_ajax_annos.py │ ├── test_permissions_ajax_presets.py │ ├── test_permissions_api.py │ ├── test_queries.py │ ├── test_query_presets.py │ ├── test_schemas.py │ ├── test_serializers_case.py │ ├── test_serializers_presets.py │ ├── test_submit_filter.py │ ├── test_sync_upstream.py │ ├── test_tasks.py │ ├── test_ui.py │ ├── test_utils.py │ ├── test_views.py │ ├── test_views_ajax.py │ ├── test_views_ajax_presets.py │ ├── test_views_api.py │ ├── test_views_api_export.py │ └── utils.py │ ├── urls │ ├── __init__.py │ ├── annos.py │ └── presets.py │ ├── utils.py │ ├── variant_stats.py │ └── views │ ├── __init__.py │ ├── ajax │ ├── __init__.py │ ├── annos.py │ └── presets.py │ └── api │ ├── __init__.py │ └── export.py ├── codecov.yml ├── docs ├── .gitattributes ├── Makefile ├── SECURITY-NPM-SUPPLY-CHAIN.md ├── __init__.py ├── _static │ └── css │ │ └── custom.css ├── admin_backup.rst ├── admin_config.rst ├── admin_extras.rst ├── admin_ingest.rst ├── admin_install.rst ├── admin_pap.rst ├── admin_tuning.rst ├── admin_update_db.rst ├── admin_upgrade.rst ├── api_beacon.rst ├── api_case.rst ├── api_importer.rst ├── api_json_schemas.rst ├── api_overview.rst ├── api_projectroles.rst ├── assets │ ├── .gitattributes │ ├── pfeiffer-quartet.ped │ ├── pfeiffer-quartet.vcf.gz │ └── pfeiffer-singleton.vcf.gz ├── conf.py ├── contributors.rst ├── databases.rst ├── figures │ ├── admin │ │ ├── admin_import.png │ │ ├── admin_login.png │ │ └── admin_view_project.png │ ├── annotation_acmg_marker.png │ ├── annotation_acmg_marker_marked.png │ ├── annotation_acmg_popup.png │ ├── annotation_case_overview.png │ ├── annotation_comments_flags_marker.png │ ├── annotation_comments_flags_marker_marked.png │ ├── annotation_comments_flags_popup.png │ ├── annotation_comments_flags_variant_details.png │ ├── case_details.png │ ├── filtration_clinvar_hgmd_tab.png │ ├── filtration_configure_download_tab.png │ ├── filtration_effects_tab.png │ ├── filtration_flags_tab.png │ ├── filtration_frequency_tab.png │ ├── filtration_gene_lists_tab.png │ ├── filtration_genotype_tab.png │ ├── filtration_miscalleneous_tab.png │ ├── filtration_quality_tab.png │ ├── filtration_results.png │ ├── filtration_settings_import_export_tab.png │ ├── igv_proxy_settings.png │ ├── kiosk_tutorial_acmg.png │ ├── kiosk_tutorial_case_annotated.png │ ├── kiosk_tutorial_case_overview.png │ ├── kiosk_tutorial_closing_case.png │ ├── kiosk_tutorial_download_xlsx.png │ ├── kiosk_tutorial_download_xlsx_process.png │ ├── kiosk_tutorial_download_xlsx_result.png │ ├── kiosk_tutorial_file_upload.png │ ├── kiosk_tutorial_filtration_results.png │ ├── kiosk_tutorial_filtration_results_detail.png │ ├── kiosk_tutorial_flagging.png │ ├── kiosk_tutorial_prioritization.png │ ├── kiosk_tutorial_prioritization_results.png │ ├── kiosk_tutorial_upload_process.png │ ├── kiosk_tutorial_variant_highlighted.png │ ├── misc_ui │ │ ├── api_tokens.png │ │ ├── import_release_info.png │ │ ├── user_menu.png │ │ └── user_profile.png │ ├── pap-structure.png │ ├── pap-structure.svg │ ├── project_details.png │ ├── search_results.png │ ├── stats_qc_case_list.png │ ├── stats_qc_plots.png │ └── varfish_home.png ├── glossary.rst ├── history.rst ├── index.rst ├── notes_clinvar.rst ├── projects_permissions.rst ├── projects_search.rst ├── release_cycle.rst ├── requirements.txt ├── smallprint.rst ├── sop_filtration.rst ├── sop_introduction.rst ├── sop_supporting.rst ├── tutorials_igv.rst ├── tutorials_kiosk.rst ├── ui_api_tokens.rst ├── ui_release_info.rst ├── ui_user_menu.rst ├── ui_user_profile.rst ├── variants_annotation.rst ├── variants_cases.rst ├── variants_filtration.rst ├── variants_project_wide.rst └── variants_stats_qc.rst ├── environment.yaml ├── frontend ├── .dockerignore ├── .editorconfig ├── .eslintignore ├── .eslintrc.cjs ├── .gitignore ├── .prettierignore ├── .prettierrc.js ├── .storybook │ ├── HomeStorybook.vue │ ├── StoryWrapper.vue │ ├── main.ts │ ├── plugins │ │ ├── index.ts │ │ ├── router.ts │ │ └── vuetify.ts │ ├── preview-head.html │ ├── preview.ts │ ├── public │ │ └── mockServiceWorker.js │ └── withVuetifyTheme.decorator.js ├── Makefile ├── babel.config.js ├── end-to-end-tests │ └── seqvar-filtration.spec.ts ├── ext │ ├── varfish-api │ │ └── src │ │ │ └── lib │ │ │ ├── @tanstack │ │ │ └── vue-query.gen.ts │ │ │ ├── index.ts │ │ │ ├── services.gen.ts │ │ │ └── types.gen.ts │ └── viguno-api │ │ ├── openapi.yaml │ │ └── src │ │ └── lib │ │ ├── @tanstack │ │ └── vue-query.gen.ts │ │ ├── index.ts │ │ ├── services.gen.ts │ │ └── types.gen.ts ├── index.html ├── jsconfig.json ├── openapi-ts.config.ts ├── openapi-ts.config.viguno.ts ├── package-lock.json ├── package.json ├── playwright.config.ts ├── src │ ├── cases │ │ ├── App.vue │ │ ├── api │ │ │ ├── caseClient.ts │ │ │ └── caseListClient.ts │ │ ├── common.js │ │ ├── common.ts │ │ ├── components │ │ │ ├── CaseDetail │ │ │ │ ├── CardAlignmentQc.vue │ │ │ │ ├── CardAnnotations.vue │ │ │ │ ├── CardCase.vue │ │ │ │ ├── CardComments.vue │ │ │ │ ├── CardGeneAnnotations.vue │ │ │ │ ├── CardPedigree.vue │ │ │ │ ├── CardQueries.vue │ │ │ │ ├── CardSvInfo.vue │ │ │ │ ├── CardTerms.vue │ │ │ │ ├── CardVariantInfo.vue │ │ │ │ ├── CardVariantQc.vue │ │ │ │ ├── Content.vue │ │ │ │ ├── FlagIcon.vue │ │ │ │ ├── PaneAnnotations.vue │ │ │ │ ├── PaneCase.vue │ │ │ │ ├── PaneQc.vue │ │ │ │ ├── QcPlotChrXRatio.vue │ │ │ │ ├── QcPlotDepthHet.vue │ │ │ │ ├── QcPlotIndelSize.vue │ │ │ │ ├── QcPlotRelatedness.vue │ │ │ │ ├── QcPlotVarEffect.vue │ │ │ │ ├── QcPlotVarType.vue │ │ │ │ ├── QcTableAlignmentStats.vue │ │ │ │ └── QcTableVarStats.vue │ │ │ ├── CaseListQc │ │ │ │ └── CaseListQc.vue │ │ │ ├── CaseListTable │ │ │ │ ├── CaseListTable.vue │ │ │ │ ├── lib.ts │ │ │ │ └── types.ts │ │ │ ├── ModalPedigreeEditor.vue │ │ │ ├── ModalPedigreeEditor │ │ │ │ └── Row.vue │ │ │ ├── ModalTermsEditor.vue │ │ │ ├── TheAppBar │ │ │ │ └── TheAppBar.vue │ │ │ └── TheNavBar │ │ │ │ └── TheNavBar.vue │ │ ├── main.ts │ │ ├── plugins │ │ │ ├── heyApi.ts │ │ │ ├── index.ts │ │ │ ├── pinia.ts │ │ │ ├── reevFrontend.ts │ │ │ └── vuetify.ts │ │ ├── queries │ │ │ ├── caseAnalysis.ts │ │ │ ├── caseAnalysisSession.ts │ │ │ └── cases.ts │ │ ├── router │ │ │ └── index.ts │ │ ├── stores │ │ │ ├── caseDetails.ts │ │ │ ├── caseList.ts │ │ │ ├── caseListQc.ts │ │ │ └── project │ │ │ │ ├── index.ts │ │ │ │ └── store.ts │ │ ├── styles │ │ │ └── main.scss │ │ └── views │ │ │ ├── CaseDetail │ │ │ ├── CaseDetail.vue │ │ │ └── CaseDetailPane.vue │ │ │ └── CaseList │ │ │ ├── CaseList.vue │ │ │ └── types.ts │ ├── cases_qc │ │ ├── api │ │ │ ├── caseQcClient.ts │ │ │ └── types.ts │ │ ├── components │ │ │ ├── DistDens.stories.data.ts │ │ │ ├── DistDens.stories.ts │ │ │ ├── DistDensPlot.vue │ │ │ ├── PaneQc.stories.data.ts │ │ │ ├── PaneQc.stories.ts │ │ │ ├── PaneQc.vue │ │ │ └── PaneQc │ │ │ │ ├── AlignmentsCoverageCard.vue │ │ │ │ ├── AlignmentsFragmentHistCard.vue │ │ │ │ ├── AlignmentsSummaryCard.vue │ │ │ │ ├── ReadsCard.vue │ │ │ │ ├── SeqvarCard.vue │ │ │ │ └── StrucvarCard.vue │ │ └── stores │ │ │ └── caseQc.ts │ ├── cohorts │ │ ├── App.vue │ │ ├── api │ │ │ └── cohorts.js │ │ ├── common.js │ │ ├── components │ │ │ ├── CohortList.vue │ │ │ ├── CohortList │ │ │ │ ├── Header.vue │ │ │ │ └── Table.vue │ │ │ └── ModalCohortEditor.vue │ │ ├── helpers.js │ │ ├── main.js │ │ └── stores │ │ │ └── cohorts.js │ ├── seqvars │ │ ├── components │ │ │ ├── GeneDataTable │ │ │ │ ├── GeneDataTable.vue │ │ │ │ └── fixture.GeneDataTable.json │ │ │ ├── PresetsEditor │ │ │ │ ├── CategoryPresetsClinvarEditor.vue │ │ │ │ ├── CategoryPresetsColumnsEditor.vue │ │ │ │ ├── CategoryPresetsConsequenceEditor.vue │ │ │ │ ├── CategoryPresetsFrequencyEditor.vue │ │ │ │ ├── CategoryPresetsLocusEditor.vue │ │ │ │ ├── CategoryPresetsPhenotypePrioEditor.vue │ │ │ │ ├── CategoryPresetsPredefinedQueriesEditor.vue │ │ │ │ ├── CategoryPresetsQualityEditor.vue │ │ │ │ ├── CategoryPresetsVariantPrioEditor.vue │ │ │ │ ├── PresetsEditor.vue │ │ │ │ ├── PresetsList.vue │ │ │ │ ├── QueryPresetsEditor.vue │ │ │ │ ├── QueryPresetsSelect.vue │ │ │ │ ├── lib │ │ │ │ │ ├── consequence.ts │ │ │ │ │ ├── index.ts │ │ │ │ │ ├── presets.ts │ │ │ │ │ ├── utils.spec.ts │ │ │ │ │ └── utils.ts │ │ │ │ └── types.ts │ │ │ ├── QueryEditor │ │ │ │ ├── ClinvarControls.vue │ │ │ │ ├── ColumnsControls.vue │ │ │ │ ├── EffectsControls.vue │ │ │ │ ├── FrequencyControls.stories.ts │ │ │ │ ├── FrequencyControls.vue │ │ │ │ ├── FrequencyControlsRow.vue │ │ │ │ ├── GenotypeControls.vue │ │ │ │ ├── InheritanceModeControls.stories.ts │ │ │ │ ├── InheritanceModeControls.vue │ │ │ │ ├── LocusControls.vue │ │ │ │ ├── PathogenicityPrioControls.vue │ │ │ │ ├── PhenotypePrioControls.vue │ │ │ │ ├── PredefinedQueryList.vue │ │ │ │ ├── PresetSummaryItem.vue │ │ │ │ ├── QualityControls.vue │ │ │ │ ├── QueryEditor.stories.ts │ │ │ │ ├── QueryEditor.vue │ │ │ │ ├── QueryList.vue │ │ │ │ ├── RecessiveControls.vue │ │ │ │ ├── SexAffectedIcon.ts │ │ │ │ ├── fixture.QueryEditor.json │ │ │ │ ├── groups.ts │ │ │ │ ├── lib │ │ │ │ │ ├── constants.ts │ │ │ │ │ ├── copy.spec.ts │ │ │ │ │ ├── copy.ts │ │ │ │ │ ├── genotype.spec.ts │ │ │ │ │ ├── genotypes.ts │ │ │ │ │ ├── index.ts │ │ │ │ │ ├── types.ts │ │ │ │ │ └── utils.ts │ │ │ │ ├── presetsDetails.FrequencyControls.json │ │ │ │ └── ui │ │ │ │ │ ├── AbbrHint.vue │ │ │ │ │ ├── CheckButton.vue │ │ │ │ │ ├── CollapsibleGroup.stories.ts │ │ │ │ │ ├── CollapsibleGroup.vue │ │ │ │ │ ├── HintButton.vue │ │ │ │ │ ├── Hr.vue │ │ │ │ │ ├── Input.vue │ │ │ │ │ ├── Item.stories.ts │ │ │ │ │ ├── Item.vue │ │ │ │ │ ├── ItemButton.vue │ │ │ │ │ ├── ModifiedIcon.vue │ │ │ │ │ ├── SelectBox.vue │ │ │ │ │ ├── SelectItem.vue │ │ │ │ │ ├── SidebarCollapseIcon.vue │ │ │ │ │ ├── SidebarExpandIcon.vue │ │ │ │ │ ├── SmallText.vue │ │ │ │ │ └── lib.ts │ │ │ ├── QueryEditorDrawer │ │ │ │ └── QueryEditorDrawer.vue │ │ │ ├── QueryResults │ │ │ │ ├── CellGeneFlags.vue │ │ │ │ ├── ClingenDosage.vue │ │ │ │ ├── QueryResults.vue │ │ │ │ ├── QueryResultsTable.vue │ │ │ │ ├── lib.ts │ │ │ │ └── types.ts │ │ │ ├── SeqvarDetails │ │ │ │ └── SeqvarDetails.vue │ │ │ └── utils.ts │ │ ├── lib │ │ │ ├── constants.ts │ │ │ └── index.ts │ │ ├── queries │ │ │ ├── seqvarQuery.ts │ │ │ ├── seqvarQueryExecution.ts │ │ │ ├── seqvarQueryPresetSet.ts │ │ │ ├── seqvarQueryPresetSetVersion.ts │ │ │ ├── seqvarQueryPresetsClinvar.ts │ │ │ ├── seqvarQueryPresetsColumns.ts │ │ │ ├── seqvarQueryPresetsConsequence.ts │ │ │ ├── seqvarQueryPresetsFrequency.ts │ │ │ ├── seqvarQueryPresetsLocus.ts │ │ │ ├── seqvarQueryPresetsPhenotypePrio.ts │ │ │ ├── seqvarQueryPresetsPredefinedQuery.ts │ │ │ ├── seqvarQueryPresetsQuality.ts │ │ │ ├── seqvarQueryPresetsVariantPrio.ts │ │ │ ├── seqvarResultRow.ts │ │ │ └── seqvarResultSet.ts │ │ ├── stores │ │ │ └── presets │ │ │ │ ├── index.ts │ │ │ │ ├── store.ts │ │ │ │ └── types.ts │ │ └── views │ │ │ ├── PresetSets │ │ │ ├── PresetSets.vue │ │ │ └── lib.ts │ │ │ └── SeqvarsQuery │ │ │ └── SeqvarsQuery.vue │ ├── svs │ │ ├── api │ │ │ └── strucvarClient │ │ │ │ ├── client.ts │ │ │ │ ├── index.ts │ │ │ │ └── types.ts │ │ ├── components │ │ │ ├── StrucvarAcmgRatingCard │ │ │ │ ├── StrucvarAcmgRatingCard.vue │ │ │ │ ├── constants.ts │ │ │ │ └── lib.ts │ │ │ ├── StrucvarDetailsHeader │ │ │ │ └── StrucvarDetailsHeader.vue │ │ │ ├── StrucvarDetailsNavi │ │ │ │ ├── StrucvarDetailsNavi.vue │ │ │ │ ├── constants.ts │ │ │ │ ├── lib.ts │ │ │ │ └── types.ts │ │ │ ├── StrucvarGenotypeCallCard │ │ │ │ ├── StrucvarGenotypeCallCard.vue │ │ │ │ ├── constants.ts │ │ │ │ └── types.ts │ │ │ ├── SvFilterApp.vue │ │ │ ├── SvFilterForm.vue │ │ │ ├── SvFilterForm │ │ │ │ ├── CriteriaDefinitionPane.vue │ │ │ │ ├── Dev.vue │ │ │ │ ├── Footer.vue │ │ │ │ ├── FrequencyPane.vue │ │ │ │ ├── GenesRegionsPane.lib.ts │ │ │ │ ├── GenesRegionsPane.vue │ │ │ │ ├── GenotypePane.vue │ │ │ │ ├── ImpactPane.fields.js │ │ │ │ ├── ImpactPane.vue │ │ │ │ ├── Patho.vue │ │ │ │ ├── QuickPresets.vue │ │ │ │ ├── RegulatoryPane.vue │ │ │ │ └── TadsPane.vue │ │ │ └── SvFilterResultsTable.vue │ │ ├── stores │ │ │ ├── strucvarFlags │ │ │ │ ├── index.ts │ │ │ │ └── store.ts │ │ │ ├── svAcmgRating.ts │ │ │ ├── svComments.ts │ │ │ ├── svDetails.ts │ │ │ ├── svQuery.js │ │ │ └── svResultSet.ts │ │ └── views │ │ │ ├── StrucvarDetails │ │ │ ├── StrucvarDetails.vue │ │ │ └── lib.ts │ │ │ └── StrucvarFilterLegacy │ │ │ └── StrucvarFilterLegacy.vue │ ├── varfish │ │ ├── api │ │ │ ├── annonars.ts │ │ │ └── mehari.ts │ │ ├── apiUtils.ts │ │ ├── common.ts │ │ ├── components │ │ │ ├── CommentsCard │ │ │ │ └── CommentsCard.vue │ │ │ ├── FilterForm │ │ │ │ └── DevPane.vue │ │ │ ├── FlagsCard │ │ │ │ ├── FlagsCard.vue │ │ │ │ └── constants.ts │ │ │ ├── ModalBase.vue │ │ │ ├── ModalConfirm.vue │ │ │ ├── ModalInput.vue │ │ │ ├── ModalSelect.vue │ │ │ ├── Overlay.vue │ │ │ ├── ScoreDisplay.stories.js │ │ │ ├── ScoreDisplay.vue │ │ │ ├── SimpleCard.vue │ │ │ ├── Toast.vue │ │ │ ├── UiToggleMaxButton │ │ │ │ └── UiToggleMaxButton.vue │ │ │ ├── VarFishLogo.vue │ │ │ ├── VariantDetails │ │ │ │ ├── FlagsIndicator.stories.js │ │ │ │ └── FlagsIndicator.vue │ │ │ └── VegaPlot.vue │ │ ├── helpers.ts │ │ ├── moreUtils.ts │ │ ├── storeUtils.ts │ │ ├── stores │ │ │ ├── ctx │ │ │ │ ├── index.ts │ │ │ │ ├── store.ts │ │ │ │ └── types.ts │ │ │ ├── history.ts │ │ │ └── ui.ts │ │ └── userSettings.ts │ └── variants │ │ ├── api │ │ ├── queryPresetsClient.ts │ │ └── variantClient │ │ │ ├── client.ts │ │ │ ├── index.ts │ │ │ └── types.ts │ │ ├── components │ │ ├── AcmgRatingCard │ │ │ ├── AcmgRatingCard.stories.ts │ │ │ ├── AcmgRatingCard.vue │ │ │ ├── constants.ts │ │ │ ├── lib.spec.ts │ │ │ ├── lib.ts │ │ │ └── types.ts │ │ ├── ColumnControl.stories.js │ │ ├── ColumnControl.vue │ │ ├── ColumnSizeFitter.stories.js │ │ ├── ColumnSizeFitter.vue │ │ ├── ExportResults.vue │ │ ├── ExportResultsButton.vue │ │ ├── FilterApp.vue │ │ ├── FilterForm.vue │ │ ├── FilterForm │ │ │ ├── ClinvarPane.stories.js │ │ │ ├── ClinvarPane.vue │ │ │ ├── EffectPane.fields.js │ │ │ ├── EffectPane.stories.js │ │ │ ├── EffectPane.vue │ │ │ ├── FlagsPane.fields.js │ │ │ ├── FlagsPane.stories.js │ │ │ ├── FlagsPane.vue │ │ │ ├── Footer.stories.js │ │ │ ├── Footer.vue │ │ │ ├── FrequencyPane.spec.ts │ │ │ ├── FrequencyPane.stories.js │ │ │ ├── FrequencyPane.vue │ │ │ ├── GenesRegionsPane.lib.ts │ │ │ ├── GenesRegionsPane.stories.js │ │ │ ├── GenesRegionsPane.vue │ │ │ ├── GenotypePane.stories.js │ │ │ ├── GenotypePane.vue │ │ │ ├── GenotypePaneAffected.stories.js │ │ │ ├── GenotypePaneAffected.vue │ │ │ ├── GenotypePaneModal.vue │ │ │ ├── GenotypePaneSex.stories.js │ │ │ ├── GenotypePaneSex.vue │ │ │ ├── PrioritizationPane.stories.js │ │ │ ├── PrioritizationPane.vue │ │ │ ├── QualityPane.stories.js │ │ │ ├── QualityPane.values.js │ │ │ ├── QualityPane.vue │ │ │ ├── QualityPaneRow.vue │ │ │ └── QuickPresets.vue │ │ ├── FilterResultsTable.vue │ │ ├── Gene.fields.ts │ │ ├── HpoTermInput.stories.js │ │ ├── HpoTermInput.values.js │ │ ├── HpoTermInput.vue │ │ ├── QueryPresets.vue │ │ ├── QueryPresets │ │ │ ├── QualityPane.vue │ │ │ ├── SetEditor.vue │ │ │ ├── SetProperties.vue │ │ │ └── SetQuickPresets.vue │ │ ├── SeqvarDetailsHeader │ │ │ └── SeqvarDetailsHeader.vue │ │ ├── SeqvarDetailsNavi │ │ │ ├── SeqvarDetailsNavi.vue │ │ │ ├── constants.ts │ │ │ ├── lib.ts │ │ │ └── types.ts │ │ ├── SeqvarGenotypeCallCard │ │ │ ├── SeqvarGenotypeCallCard.stories.js │ │ │ ├── SeqvarGenotypeCallCard.vue │ │ │ ├── lib.ts │ │ │ └── types.ts │ │ ├── TokenizingTextarea.stories.js │ │ └── TokenizingTextarea.vue │ │ ├── enums.ts │ │ ├── helpers.js │ │ ├── stores │ │ ├── queryPresets.ts │ │ ├── variantAcmgRating │ │ │ ├── index.ts │ │ │ └── store.ts │ │ ├── variantComments.ts │ │ ├── variantDetails.ts │ │ ├── variantFlags.ts │ │ ├── variantQuery.funcs.js │ │ ├── variantQuery.js │ │ └── variantResultSet.ts │ │ └── views │ │ ├── SeqvarDetails │ │ └── SeqvarDetails.vue │ │ └── SeqvarFilterLegacy │ │ └── SeqvarFilterLegacy.vue ├── tests │ ├── cases │ │ ├── data │ │ │ ├── caseDetailsStoreData.json │ │ │ ├── caseListResponse.json │ │ │ ├── caseListStoreData.json │ │ │ ├── casesQcStoreData.json │ │ │ ├── fetchCaseAlignmentStatsResponse.json │ │ │ ├── fetchCaseRelatednessResponse.json │ │ │ ├── fetchCaseVariantStatsResponse.json │ │ │ └── loadProjectQcValuesResponse.json │ │ ├── helpers.js │ │ └── unit │ │ │ └── cases │ │ │ ├── CaseDetail │ │ │ ├── CardAlignmentQc.spec.js │ │ │ ├── CardAnnotations.spec.js │ │ │ ├── CardCase.spec.js │ │ │ ├── CardComments.spec.js │ │ │ ├── CardGeneAnnotations.spec.js │ │ │ ├── CardPedigree.spec.js │ │ │ ├── CardSvInfo.spec.js │ │ │ ├── CardTerms.spec.js │ │ │ ├── CardVariantInfo.spec.js │ │ │ ├── CardVariantQc.spec.js │ │ │ ├── FlagIcon.spec.js │ │ │ ├── PaneCase.spec.js │ │ │ ├── PaneQc.spec.js │ │ │ └── QcTableVarStats.spec.js │ │ │ ├── CaseDetailApp.common.js │ │ │ └── Overlay.spec.js │ ├── cohorts │ │ ├── data │ │ │ ├── accessibleProjectsCasesResponse.json │ │ │ ├── cohortsStoreData.json │ │ │ ├── createCohortCaseResponses.json │ │ │ ├── createCohortResponse.json │ │ │ ├── listCohortAfterCreateResponse.json │ │ │ ├── listCohortAfterUpdateResponse.json │ │ │ ├── listCohortCaseResponse.json │ │ │ ├── listCohortResponse.json │ │ │ ├── permissionsResponse.json │ │ │ └── updateCohortResponse.json │ │ ├── helpers.js │ │ └── unit │ │ │ ├── App.spec.js │ │ │ ├── api │ │ │ └── cohorts.spec.js │ │ │ ├── components │ │ │ ├── CohortList.spec.js │ │ │ ├── CohortList │ │ │ │ ├── Header.spec.js │ │ │ │ └── Table.spec.js │ │ │ └── ModalCohortEditor.spec.js │ │ │ └── stores │ │ │ └── cohorts.spec.js │ ├── varfish │ │ └── unit │ │ │ └── VegaPlot.spec.js │ └── variants │ │ ├── data │ │ ├── case-singleton.json │ │ ├── case-trio.json │ │ ├── export-settings-singleton.json │ │ ├── export-settings-trio.json │ │ ├── filter-query-store.json │ │ ├── gene-brca1-geneinfo.json │ │ ├── gene-mtdna-geneinfo.json │ │ ├── known-gene-aa.json │ │ ├── listChromosomePresetsResponse.json │ │ ├── listFlagsEtcPresetsResponse.json │ │ ├── listFrequencyPresetsResponse.json │ │ ├── listImpactPresetsResponse.json │ │ ├── listPresetSetResponse.json │ │ ├── listQualityPresetsResponse.json │ │ ├── listQueryResultRowResult.json │ │ ├── listQueryResultSetResult.json │ │ ├── listQuickPresetsResponse.json │ │ ├── localPanelResponse.json │ │ ├── lookup-gene-response.json │ │ ├── panelapp-response-page1.json │ │ ├── panelapp-response-page2.json │ │ ├── panelapp-response-page3.json │ │ ├── panelapp-response-page4.json │ │ ├── query-settings-singleton.json │ │ ├── query-settings-trio.json │ │ ├── retrieveChromosomePresetsResponse.json │ │ ├── retrieveFlagsEtcPresetsResponse.json │ │ ├── retrieveFrequencyPresetsResponse.json │ │ ├── retrieveImpactPresetsResponse.json │ │ ├── retrievePresetSetResponse.json │ │ ├── retrieveQualityPresetsResponse.json │ │ ├── retrieveQuickPresetsResponse.json │ │ ├── var-brca1-missense-benign-smallvar.json │ │ ├── var-brca1-missense-benign-txcsq.json │ │ ├── var-brca1-missense-benign-varannos.json │ │ ├── var-mtdna-noncoding-smallvar.json │ │ ├── variant-details-store.json │ │ ├── variant-validator.json │ │ └── variants-trio.json │ │ └── unit │ │ ├── components │ │ ├── ColumnControl.spec.js │ │ ├── ColumnSizeFitter.spec.js │ │ ├── FilterForm │ │ │ ├── ClinvarPane.spec.js │ │ │ ├── EffectPane.spec.js │ │ │ ├── FlagsPane.spec.js │ │ │ ├── Footer.spec.js │ │ │ ├── FrequencyPane.spec.js │ │ │ ├── GenesRegionsPane.spec.js │ │ │ ├── GenotypePane.spec.js │ │ │ ├── GenotypePaneAffected.spec.js │ │ │ ├── GenotypePaneModal.spec.js │ │ │ ├── GenotypePaneSex.spec.js │ │ │ ├── PrioritizationPane.spec.js │ │ │ ├── QualityPane.spec.js │ │ │ ├── QualityPaneRow.spec.js │ │ │ └── QuickPresets.spec.js │ │ ├── FilterResultsTable.spec.js │ │ ├── HpoTermInput.spec.js │ │ ├── TokenizingTextarea.spec.js │ │ └── VariantDetails │ │ │ ├── CallDetails.spec.js │ │ │ ├── Clinvar.spec.js │ │ │ ├── CommentsFlags.spec.js │ │ │ ├── CommentsFlagsIndicator.spec.js │ │ │ ├── Conservation.spec.js │ │ │ ├── Freqs.spec.js │ │ │ ├── Ga4ghBeacons.spec.js │ │ │ └── Gene.spec.js │ │ └── stores │ │ ├── filterQuery.spec.js │ │ └── variantDetails.spec.js ├── tsconfig.json ├── tsconfig.node.json └── vite.config.js ├── release-please-config.json └── utils ├── docker ├── .gitignore ├── Dockerfile ├── build-docker.sh └── docker-entrypoint.sh ├── install_backend_os_dependencies.sh ├── install_chrome.sh ├── install_chrome_gitlab.sh ├── install_frontend_os_dependencies.sh ├── install_ldap_dependencies.sh ├── install_os_gitlab.sh ├── install_python_dependencies.sh ├── kickoff_orphaned_annotation_query.py ├── npm-security-check.sh ├── projectwide_query.py ├── quick_presets_to_docx.py ├── requirements-jessie.apt ├── requirements-trusty.apt ├── requirements-xenial.apt ├── scan-npm-compromise.sh ├── setup_database.sh └── terraform ├── .gitignore ├── main.tf └── provider.tf /.dockerignore: -------------------------------------------------------------------------------- 1 | .git 2 | median/* 3 | node_modules/* 4 | -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/varfish-org/varfish-server/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitattributes: 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