CHANGELOG.md
LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
scout/__init__.py
scout/__version__.py
scout/adapter/__init__.py
scout/adapter/client.py
scout/adapter/utils.py
scout/adapter/mongo/__init__.py
scout/adapter/mongo/acmg.py
scout/adapter/mongo/base.py
scout/adapter/mongo/case.py
scout/adapter/mongo/case_events.py
scout/adapter/mongo/clinvar.py
scout/adapter/mongo/event.py
scout/adapter/mongo/hgnc.py
scout/adapter/mongo/hpo.py
scout/adapter/mongo/index.py
scout/adapter/mongo/institute.py
scout/adapter/mongo/panel.py
scout/adapter/mongo/query.py
scout/adapter/mongo/user.py
scout/adapter/mongo/variant.py
scout/adapter/mongo/variant_events.py
scout/adapter/mongo/variant_loader.py
scout/build/__init__.py
scout/build/acmg.py
scout/build/case.py
scout/build/disease.py
scout/build/hpo.py
scout/build/individual.py
scout/build/institute.py
scout/build/panel.py
scout/build/phenotype.py
scout/build/user.py
scout/build/genes/__init__.py
scout/build/genes/exon.py
scout/build/genes/hgnc_gene.py
scout/build/genes/transcript.py
scout/build/variant/__init__.py
scout/build/variant/clnsig.py
scout/build/variant/compound.py
scout/build/variant/gene.py
scout/build/variant/genotype.py
scout/build/variant/transcript.py
scout/build/variant/variant.py
scout/commands/__init__.py
scout/commands/base.py
scout/commands/convert.py
scout/commands/index_command.py
scout/commands/serve.py
scout/commands/utils.py
scout/commands/wipe_database.py
scout/commands/delete/__init__.py
scout/commands/delete/delete_command.py
scout/commands/export/__init__.py
scout/commands/export/case.py
scout/commands/export/export_command.py
scout/commands/export/gene.py
scout/commands/export/hpo.py
scout/commands/export/mitochondrial_report.py
scout/commands/export/panel.py
scout/commands/export/transcript.py
scout/commands/export/utils.py
scout/commands/export/variant.py
scout/commands/load/__init__.py
scout/commands/load/base.py
scout/commands/load/case.py
scout/commands/load/exons.py
scout/commands/load/institute.py
scout/commands/load/panel.py
scout/commands/load/region.py
scout/commands/load/report.py
scout/commands/load/research.py
scout/commands/load/user.py
scout/commands/load/variants.py
scout/commands/query/__init__.py
scout/commands/query/query_command.py
scout/commands/setup/__init__.py
scout/commands/setup/setup_scout.py
scout/commands/update/__init__.py
scout/commands/update/base.py
scout/commands/update/case.py
scout/commands/update/compounds.py
scout/commands/update/disease.py
scout/commands/update/genes.py
scout/commands/update/hpo.py
scout/commands/update/institute.py
scout/commands/update/omim.py
scout/commands/update/panel.py
scout/commands/update/phenotype_groups.py
scout/commands/update/user.py
scout/commands/view/__init__.py
scout/commands/view/aliases.py
scout/commands/view/base.py
scout/commands/view/case.py
scout/commands/view/collections.py
scout/commands/view/diseases.py
scout/commands/view/hpo.py
scout/commands/view/index.py
scout/commands/view/individuals.py
scout/commands/view/institutes.py
scout/commands/view/intervals.py
scout/commands/view/panels.py
scout/commands/view/transcripts.py
scout/commands/view/users.py
scout/commands/view/whitelist.py
scout/constants/__init__.py
scout/constants/acmg.py
scout/constants/case_tags.py
scout/constants/clinvar.py
scout/constants/clnsig.py
scout/constants/file_types.py
scout/constants/indexes.py
scout/constants/phenotype.py
scout/constants/so_terms.py
scout/constants/variant_tags.py
scout/constants/variants_export.py
scout/demo/643594.clinical.SV.vcf.gz
scout/demo/643594.clinical.SV.vcf.gz.tbi
scout/demo/643594.clinical.str.annotated.vcf.gz
scout/demo/643594.clinical.str.annotated.vcf.gz.tbi
scout/demo/643594.clinical.str.vcf.gz
scout/demo/643594.clinical.str.vcf.gz.tbi
scout/demo/643594.clinical.vcf.gz
scout/demo/643594.clinical.vcf.gz.tbi
scout/demo/643594.config.yaml
scout/demo/643594.ped
scout/demo/643594.ped_check.csv
scout/demo/643594.peddy.ped
scout/demo/643594.research.SV.vcf.gz
scout/demo/643594.research.SV.vcf.gz.tbi
scout/demo/643594.research.vcf.gz
scout/demo/643594.research.vcf.gz.tbi
scout/demo/643594.sex_check.csv
scout/demo/643595.config.yaml
scout/demo/ADM1059A1.dummy.cgh
scout/demo/ADM1059A2.dummy.cgh
scout/demo/ADM1059A3.dummy.cgh
scout/demo/__init__.py
scout/demo/cancer_test.ped
scout/demo/cancer_test.vcf.gz
scout/demo/cancer_test.vcf.gz.tbi
scout/demo/chanjo4_demo.sql
scout/demo/delivery_report.html
scout/demo/madeline.xml
scout/demo/panel_1.bed
scout/demo/panel_1.csv
scout/demo/panel_1.txt
scout/demo/reduced_mt.bam
scout/demo/reduced_mt.bam.bai
scout/demo/resources/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes_reduced.txt
scout/demo/resources/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype_reduced.txt
scout/demo/resources/ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes_reduced.txt
scout/demo/resources/__init__.py
scout/demo/resources/chanjo4_structure.sql
scout/demo/resources/ensembl_genes_37_reduced.txt
scout/demo/resources/ensembl_genes_38_reduced.txt
scout/demo/resources/ensembl_transcripts_37_reduced.txt
scout/demo/resources/ensembl_transcripts_38_reduced.txt
scout/demo/resources/forweb_cleaned_exac_r03_march16_z_data_pLI_reduced.txt
scout/demo/resources/genemap2_reduced.txt
scout/demo/resources/generate_test_data.py
scout/demo/resources/hgnc_reduced_set.txt
scout/demo/resources/hpo_terms.csv
scout/demo/resources/mim2gene_reduced.txt
scout/demo/resources/reduced.hpo.obo
scout/exceptions/__init__.py
scout/exceptions/config.py
scout/exceptions/database.py
scout/exceptions/pedigree.py
scout/exceptions/vcf.py
scout/export/__init__.py
scout/export/gene.py
scout/export/panel.py
scout/export/transcript.py
scout/export/variant.py
scout/load/__init__.py
scout/load/all.py
scout/load/case.py
scout/load/exon.py
scout/load/hgnc_gene.py
scout/load/hpo.py
scout/load/institute.py
scout/load/panel.py
scout/load/report.py
scout/load/setup.py
scout/load/transcript.py
scout/log/__init__.py
scout/log/handlers.py
scout/log/log.py
scout/models/__init__.py
scout/models/acmg_evaluation.py
scout/models/event.py
scout/models/hgnc_map.py
scout/models/institute.py
scout/models/panel.py
scout/models/phenotype_term.py
scout/models/user.py
scout/models/whitelist.py
scout/models/case/__init__.py
scout/models/case/case.py
scout/models/variant/__init__.py
scout/models/variant/gene.py
scout/models/variant/transcript.py
scout/models/variant/variant.py
scout/parse/__init__.py
scout/parse/case.py
scout/parse/clinvar.py
scout/parse/cytoband.py
scout/parse/ensembl.py
scout/parse/exac.py
scout/parse/hgnc.py
scout/parse/hpo.py
scout/parse/omim.py
scout/parse/panel.py
scout/parse/peddy.py
scout/parse/variant/__init__.py
scout/parse/variant/callers.py
scout/parse/variant/clnsig.py
scout/parse/variant/compound.py
scout/parse/variant/conservation.py
scout/parse/variant/coordinates.py
scout/parse/variant/deleteriousness.py
scout/parse/variant/frequency.py
scout/parse/variant/gene.py
scout/parse/variant/genotype.py
scout/parse/variant/headers.py
scout/parse/variant/ids.py
scout/parse/variant/models.py
scout/parse/variant/rank_score.py
scout/parse/variant/transcript.py
scout/parse/variant/variant.py
scout/resources/__init__.py
scout/resources/cytoBand.txt.gz
scout/server/__init__.py
scout/server/app.py
scout/server/auto.py
scout/server/config.py
scout/server/extensions.py
scout/server/links.py
scout/server/userpanel.py
scout/server/utils.py
scout/server/blueprints/__init__.py
scout/server/blueprints/alignviewers/__init__.py
scout/server/blueprints/alignviewers/partial.py
scout/server/blueprints/alignviewers/views.py
scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html
scout/server/blueprints/alignviewers/templates/alignviewers/pileup.html
scout/server/blueprints/api/__init__.py
scout/server/blueprints/api/views.py
scout/server/blueprints/cases/__init__.py
scout/server/blueprints/cases/controllers.py
scout/server/blueprints/cases/views.py
scout/server/blueprints/cases/static/madeline.js
scout/server/blueprints/cases/templates/cases/actionbar.html
scout/server/blueprints/cases/templates/cases/case.html
scout/server/blueprints/cases/templates/cases/case_report.html
scout/server/blueprints/cases/templates/cases/cases.html
scout/server/blueprints/cases/templates/cases/causatives.html
scout/server/blueprints/cases/templates/cases/clinvar_submissions.html
scout/server/blueprints/cases/templates/cases/diseases.html
scout/server/blueprints/cases/templates/cases/index.html
scout/server/blueprints/dashboard/__init__.py
scout/server/blueprints/dashboard/controllers.py
scout/server/blueprints/dashboard/views.py
scout/server/blueprints/dashboard/templates/dashboard/index.html
scout/server/blueprints/genes/__init__.py
scout/server/blueprints/genes/controllers.py
scout/server/blueprints/genes/views.py
scout/server/blueprints/genes/templates/genes/gene.html
scout/server/blueprints/genes/templates/genes/genes.html
scout/server/blueprints/genes/templates/genes/layout.html
scout/server/blueprints/institutes/__init__.py
scout/server/blueprints/institutes/views.py
scout/server/blueprints/institutes/templates/overview/institutes.html
scout/server/blueprints/login/__init__.py
scout/server/blueprints/login/controllers.py
scout/server/blueprints/login/models.py
scout/server/blueprints/login/views.py
scout/server/blueprints/login/static/commander.svg
scout/server/blueprints/login/static/commissioner.svg
scout/server/blueprints/login/static/constable.svg
scout/server/blueprints/login/static/inspector.svg
scout/server/blueprints/login/static/sergeant.svg
scout/server/blueprints/login/static/superintendent.svg
scout/server/blueprints/login/templates/login/users.html
scout/server/blueprints/panels/__init__.py
scout/server/blueprints/panels/controllers.py
scout/server/blueprints/panels/forms.py
scout/server/blueprints/panels/views.py
scout/server/blueprints/panels/templates/panels/gene-edit.html
scout/server/blueprints/panels/templates/panels/panel.html
scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html
scout/server/blueprints/panels/templates/panels/panels.html
scout/server/blueprints/phenotypes/__init__.py
scout/server/blueprints/phenotypes/controllers.py
scout/server/blueprints/phenotypes/views.py
scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html
scout/server/blueprints/public/__init__.py
scout/server/blueprints/public/views.py
scout/server/blueprints/public/static/logo-karolinska.png
scout/server/blueprints/public/static/logo-scilifelab.png
scout/server/blueprints/public/static/scout-logo.png
scout/server/blueprints/public/static/swedac.png
scout/server/blueprints/public/templates/public/index.html
scout/server/blueprints/variants/__init__.py
scout/server/blueprints/variants/controllers.py
scout/server/blueprints/variants/forms.py
scout/server/blueprints/variants/views.py
scout/server/blueprints/variants/templates/variants/acmg.html
scout/server/blueprints/variants/templates/variants/cancer-variants.html
scout/server/blueprints/variants/templates/variants/clinvar.html
scout/server/blueprints/variants/templates/variants/components.html
scout/server/blueprints/variants/templates/variants/layout.html
scout/server/blueprints/variants/templates/variants/str-variant.html
scout/server/blueprints/variants/templates/variants/str-variants.html
scout/server/blueprints/variants/templates/variants/sv-variant.html
scout/server/blueprints/variants/templates/variants/sv-variants.html
scout/server/blueprints/variants/templates/variants/utils.html
scout/server/blueprints/variants/templates/variants/variant.html
scout/server/blueprints/variants/templates/variants/variants.html
scout/server/static/favicon.ico
scout/server/static/humans.txt
scout/server/static/robots.txt
scout/server/static/styles.css
scout/server/templates/layout.html
scout/server/templates/report_base.html
scout/server/templates/utils.html
scout/server/translations/sv/LC_MESSAGES/messages.mo
scout/server/translations/sv/LC_MESSAGES/messages.po
scout/update/__init__.py
scout/update/panel.py
scout/utils/__init__.py
scout/utils/acmg.py
scout/utils/convert.py
scout/utils/coordinates.py
scout/utils/date.py
scout/utils/gene.py
scout/utils/handle.py
scout/utils/hgnc_id.py
scout/utils/link.py
scout/utils/md5.py
scout/utils/requests.py
scout_browser.egg-info/PKG-INFO
scout_browser.egg-info/SOURCES.txt
scout_browser.egg-info/dependency_links.txt
scout_browser.egg-info/entry_points.txt
scout_browser.egg-info/not-zip-safe
scout_browser.egg-info/requires.txt
scout_browser.egg-info/top_level.txt
tests/conftest.py
tests/adapter/conftest.py
tests/adapter/mongo/test_adapter_variant_caseid.py
tests/adapter/mongo/test_case_handling.py
tests/adapter/mongo/test_clinvar_handler.py
tests/adapter/mongo/test_comment_handling.py
tests/adapter/mongo/test_connect.py
tests/adapter/mongo/test_evaluated_variants.py
tests/adapter/mongo/test_event_handling.py
tests/adapter/mongo/test_gene_handler.py
tests/adapter/mongo/test_hpo_handler.py
tests/adapter/mongo/test_index_handling.py
tests/adapter/mongo/test_institute_handler.py
tests/adapter/mongo/test_panel_handler.py
tests/adapter/mongo/test_query.py
tests/adapter/mongo/test_sanger_validation.py
tests/adapter/mongo/test_update_synopsis
tests/adapter/mongo/test_user_handling.py
tests/adapter/mongo/test_variant_events.py
tests/adapter/mongo/test_variant_handling.py
tests/build/test_build_case.py
tests/build/test_build_clnsig.py
tests/build/test_build_disease.py
tests/build/test_build_exon.py
tests/build/test_build_gene.py
tests/build/test_build_hgnc_gene.py
tests/build/test_build_hgnc_transcript.py
tests/build/test_build_hpo.py
tests/build/test_build_individual.py
tests/build/test_build_institute.py
tests/build/test_build_panel.py
tests/build/test_build_user.py
tests/build/test_build_variant.py
tests/commands/test_base_command.py
tests/commands/test_delete_case_cmd.py
tests/commands/test_load_case_cmd.py
tests/commands/test_load_institute_cmd.py
tests/commands/test_wipe_database.py
tests/export/test_export_variants.py
tests/load/test_load_case.py
tests/load/test_load_hgnc_genes.py
tests/load/test_load_hpo.py
tests/load/test_load_institute.py
tests/load/test_load_panel.py
tests/load/test_load_report.py
tests/load/test_load_transcripts.py
tests/load/test_load_variant.py
tests/load/test_setup_scout.py
tests/parse/test_frequency.py
tests/parse/test_ids.py
tests/parse/test_parse_callers.py
tests/parse/test_parse_case.py
tests/parse/test_parse_clinvar_form.py
tests/parse/test_parse_clnsig.py
tests/parse/test_parse_compounds.py
tests/parse/test_parse_conservation.py
tests/parse/test_parse_coordinates.py
tests/parse/test_parse_ensembl_transcripts.py
tests/parse/test_parse_exac_genes.py
tests/parse/test_parse_genes.py
tests/parse/test_parse_genotype.py
tests/parse/test_parse_headers.py
tests/parse/test_parse_hgnc.py
tests/parse/test_parse_hpo_disease.py
tests/parse/test_parse_hpo_genes.py
tests/parse/test_parse_hpo_terms.py
tests/parse/test_parse_omim.py
tests/parse/test_parse_panel.py
tests/parse/test_parse_rank_score.py
tests/parse/test_parse_transcripts.py
tests/parse/test_parse_variant.py
tests/parse/vcfs/one_cnvnator.vcf
tests/server/conftest.py
tests/server/test_server_genes.py
tests/server/test_server_panels.py
tests/server/test_server_public.py
tests/server/blueprints/dashboard/test_dashboard_controllers.py
tests/server/blueprints/variants/conftest.py
tests/server/blueprints/variants/test_controllers.py
tests/update/test_update_compounds.py
tests/update/test_update_institute.py
tests/update/test_update_panel.py
tests/utils/test_acmg.py
tests/utils/test_date.py
tests/utils/test_link_genes.py
tests/utils/test_par.py