LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
covigator/__init__.py
covigator/command_line.py
covigator/configuration.py
covigator/exceptions.py
covigator/wsgi.py
covigator.egg-info/PKG-INFO
covigator.egg-info/SOURCES.txt
covigator.egg-info/dependency_links.txt
covigator.egg-info/entry_points.txt
covigator.egg-info/requires.txt
covigator.egg-info/top_level.txt
covigator/accessor/__init__.py
covigator/accessor/ena_accessor.py
covigator/accessor/gisaid_accessor.py
covigator/dashboard/__init__.py
covigator/dashboard/dashboard.py
covigator/dashboard/assets/2021_twitter_logo_blue.png
covigator/dashboard/assets/CoVigator_ico.png
covigator/dashboard/assets/CoVigator_logo.png
covigator/dashboard/assets/CoVigator_logo_ENA.png
covigator/dashboard/assets/CoVigator_logo_GISAID.png
covigator/dashboard/assets/CoVigator_logo_GISAID_ENA.png
covigator/dashboard/assets/CoVigator_logo_txt.png
covigator/dashboard/assets/CoVigator_logo_txt_nobg.png
covigator/dashboard/assets/CoVigator_logo_txt_reg.png
covigator/dashboard/assets/CoVigator_logo_txt_reg_no_bg.png
covigator/dashboard/assets/CoVigator_logo_txt_reg_no_bg_ena.xcf
covigator/dashboard/assets/CoVigator_logo_txt_reg_no_bg_gisaid.xcf
covigator/dashboard/assets/CoVigator_logo_txt_reg_no_bg_gisaid_and_ena.xcf
covigator/dashboard/assets/ENA_logo_2021.png
covigator/dashboard/assets/ENA_logo_2021_wo_text.png
covigator/dashboard/assets/favicon.ico
covigator/dashboard/assets/favicon___.ico
covigator/dashboard/assets/gisaid.png
covigator/dashboard/assets/resizing_script.js
covigator/dashboard/assets/s1.css
covigator/dashboard/assets/styles.css
covigator/dashboard/assets/tron_logo.png
covigator/dashboard/assets/tron_logo_no_bg.png
covigator/dashboard/assets/tron_logo_without_text.png
covigator/dashboard/figures/__init__.py
covigator/dashboard/figures/figures.py
covigator/dashboard/figures/intrahost_mutations.py
covigator/dashboard/figures/lineages.py
covigator/dashboard/figures/mutation_stats.py
covigator/dashboard/figures/recurrent_mutations.py
covigator/dashboard/figures/samples.py
covigator/dashboard/tabs/__init__.py
covigator/dashboard/tabs/acknowledgements.py
covigator/dashboard/tabs/dataset_ena.py
covigator/dashboard/tabs/dataset_gisaid.py
covigator/dashboard/tabs/download.py
covigator/dashboard/tabs/footer.py
covigator/dashboard/tabs/intrahost_mutations.py
covigator/dashboard/tabs/lineages.py
covigator/dashboard/tabs/mutation_stats.py
covigator/dashboard/tabs/overview.py
covigator/dashboard/tabs/recurrent_mutations.py
covigator/dashboard/tabs/samples.py
covigator/database/__init__.py
covigator/database/database.py
covigator/database/model.py
covigator/database/queries.py
covigator/misc/__init__.py
covigator/misc/backoff_retrier.py
covigator/misc/compression.py
covigator/misc/country_parser.py
covigator/pipeline/__init__.py
covigator/pipeline/cooccurrence_matrix.py
covigator/pipeline/downloader.py
covigator/pipeline/ena_pipeline.py
covigator/pipeline/gisaid_pipeline.py
covigator/pipeline/runner.py
covigator/pipeline/vcf_loader.py
covigator/precomputations/__init__.py
covigator/precomputations/load_cooccurrences.py
covigator/precomputations/load_ns_s_counts.py
covigator/precomputations/load_top_occurrences.py
covigator/precomputations/load_variants_per_lineage.py
covigator/precomputations/loader.py
covigator/processor/__init__.py
covigator/processor/abstract_processor.py
covigator/processor/ena_downloader.py
covigator/processor/ena_processor.py
covigator/processor/gisaid_processor.py
covigator/references/__init__.py
covigator/references/conservation.py
covigator/references/domains_NS_S.csv
covigator/references/gene_annotations.py
covigator/references/genes_NS_S.csv
covigator/references/sars_cov_2.json
covigator/references/wuhCor1.mutDepletionConsHMM.bed
covigator/references/wuhCor1.mutDepletionSarbecovirusConsHMM.bed
covigator/references/wuhCor1.mutDepletionVertebrateCoVConsHMM.bed
covigator/tests/__init__.py
covigator/tests/integration_tests/__init__.py
covigator/tests/integration_tests/integration_tests.py
covigator/tests/integration_tests/test_downloader.py
covigator/tests/integration_tests/test_gene_annotations.py
covigator/tests/integration_tests/test_gisaid_accessor.py
covigator/tests/integration_tests/test_pipeline.py
covigator/tests/integration_tests/test_vcf_loader.py
covigator/tests/resources/MN908947.3.fa
covigator/tests/resources/Sars_cov_2.ASM985889v3.pep.all.fa
covigator/tests/resources/Sars_cov_2.all_variants.snpeff.vcf.gz
covigator/tests/resources/Sars_cov_2.all_variants.snpeff.vcf.gz.tbi
covigator/tests/resources/domains_NS_S.csv
covigator/tests/resources/genes_NS_S.csv
covigator/tests/resources/gisaid_allprot0526.fasta
covigator/tests/resources/gisaid_allprot1208.fasta
covigator/tests/resources/gisaid_allprot1208.with_mutations.fasta
covigator/tests/resources/sars_cov_2.json
covigator/tests/resources/sars_cov_2_dn_ds.json
covigator/tests/resources/snpeff.vcf
covigator/tests/resources/snpeff_with_deletion.vcf
covigator/tests/resources/snpeff_with_insertion.vcf
covigator/tests/resources/snpeff_without_annotation.vcf
covigator/tests/resources/snpeff_without_dp4.vcf
covigator/tests/resources/test.assembly.vcf.gz
covigator/tests/resources/test.assembly.vcf.gz.tbi
covigator/tests/resources/test.coverage.tsv
covigator/tests/resources/test.deduplication_metrics.txt
covigator/tests/resources/test.lofreq.pangolin.csv
covigator/tests/resources/test.lofreq.pangolin.with_none.csv
covigator/tests/resources/test.lofreq.vcf.gz
covigator/tests/resources/test.lofreq.vcf.gz.tbi
covigator/tests/resources/test_data.fasta
covigator/tests/unit_tests/__init__.py
covigator/tests/unit_tests/abstract_test.py
covigator/tests/unit_tests/faked_objects.py
covigator/tests/unit_tests/mocked.py
covigator/tests/unit_tests/test_compression.py
covigator/tests/unit_tests/test_cooccurrence_matrix.py
covigator/tests/unit_tests/test_country_parser.py
covigator/tests/unit_tests/test_database_initialisation.py
covigator/tests/unit_tests/test_downloader.py
covigator/tests/unit_tests/test_ena_accessor.py
covigator/tests/unit_tests/test_figures.py
covigator/tests/unit_tests/test_precomputer.py
covigator/tests/unit_tests/test_processor.py
covigator/tests/unit_tests/test_queries.py
covigator/tests/unit_tests/test_vcf_loader.py