├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── pythonapp.yml ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── etc ├── annotate_vep │ ├── make_vcf.py │ ├── merge.py │ └── run.sh ├── demo.md ├── detailed-apache2-instructions │ ├── README.md │ └── pheweb.conf ├── detailed-development-instructions.md ├── detailed-install-instructions.md ├── detailed-internal-dataflow.md ├── detailed-loading-instructions.md ├── detailed-webserver-instructions.md ├── images │ ├── screen-homepage-search.png │ ├── screen-homepage.png │ ├── screen-lz-tooltip.png │ ├── screen-lz.png │ ├── screen-manhattan.png │ ├── screen-phewas.png │ └── screen-qq.png ├── make-input-file.py ├── phecode_icd9 │ ├── make_phecode_icd9.py │ └── phecodes_icd9.json ├── pheweb.service └── pre-commit ├── pheweb ├── __init__.py ├── command_line.py ├── conf.py ├── file_utils.py ├── load │ ├── __init__.py │ ├── add_genes.py │ ├── add_rsids.py │ ├── augment_phenos.py │ ├── best_of_pheno.py │ ├── cffi │ │ ├── ffibuilder.py │ │ └── x.cpp │ ├── cluster.py │ ├── detect_ref.py │ ├── download_genes.py │ ├── download_genes_from_scratch.py │ ├── download_rsids.py │ ├── download_rsids_from_scratch.py │ ├── gather_pvalues_for_each_gene.py │ ├── load_utils.py │ ├── make_cpras_rsids_sqlite3.py │ ├── make_gene_aliases_sqlite3.py │ ├── manhattan.py │ ├── matrix.py │ ├── parse_input_files.py │ ├── pheno_correlation.py │ ├── phenolist │ │ └── __init__.py │ ├── phenotypes.py │ ├── process_assoc_files.py │ ├── qq.py │ ├── read_input_file.py │ ├── sites.py │ ├── top_hits.py │ ├── top_loci.py │ └── wsgi.py ├── parse_utils.py ├── serve │ ├── __init__.py │ ├── auth.py │ ├── autocomplete.py │ ├── run.py │ ├── server.py │ ├── server_utils.py │ ├── static │ │ ├── common.css │ │ ├── common.js │ │ ├── fonts │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ └── glyphicons-halflings-regular.woff2 │ │ ├── gene.js │ │ ├── pheno-filter.js │ │ ├── pheno.js │ │ ├── phenotypes.js │ │ ├── region.css │ │ ├── region.js │ │ ├── top_hits.js │ │ ├── variant.js │ │ └── vendor │ │ │ └── stream_table-1.1.1.min.js │ └── templates │ │ ├── about.html │ │ ├── about │ │ └── content.html │ │ ├── error.html │ │ ├── gene.html │ │ ├── index.html │ │ ├── index │ │ ├── below-h1.html │ │ ├── below-query.html │ │ └── h1.html │ │ ├── layout.html │ │ ├── pheno-filter.html │ │ ├── pheno.html │ │ ├── pheno │ │ ├── h1.html │ │ └── info.html │ │ ├── phenotypes.html │ │ ├── region.html │ │ ├── region │ │ └── h1.html │ │ ├── title.html │ │ ├── top_hits.html │ │ └── variant.html ├── utils.py ├── version.py └── weetabix.py ├── setup.cfg ├── setup.py └── tests ├── in_venv.sh ├── input_files ├── assoc-files │ ├── *&\+. !`(%@).epacts.gz │ ├── EAR-LENGTH.epacts.gz │ ├── has-fields-.txt │ ├── has-fields-ac-af-maf-ns.txt │ ├── has-fields-ac-af-maf.txt │ ├── has-fields-ac-af-ns.txt │ ├── has-fields-ac-af.txt │ ├── has-fields-ac-maf-ns.txt │ ├── has-fields-ac-maf.txt │ ├── has-fields-ac-ns.txt │ ├── has-fields-ac.txt │ ├── has-fields-af-maf-ns.txt │ ├── has-fields-af-maf.txt │ ├── has-fields-af-ns.txt │ ├── has-fields-af.txt │ ├── has-fields-maf-ns.txt │ ├── has-fields-maf.txt │ ├── has-fields-ns.txt │ ├── pheno.0 │ ├── pheno.1.tsv │ ├── pheno.3.1.epacts.gz │ ├── pheno2.chr1.tsv │ ├── pheno2.chr19.tsv │ └── snowstorm.txt ├── categories.csv ├── config.py ├── correlations │ ├── pheno-correlations.txt │ ├── pheno-list.json │ └── rg-pipeline-output.txt ├── custom_templates │ └── index │ │ └── below-h1.html ├── fake-cache │ ├── gene_aliases-v36.sqlite3 │ ├── gene_aliases-v37.sqlite3 │ ├── genes-v36-hg19.bed │ ├── genes-v37-hg19.bed │ ├── rsids-v150-hg19.tsv.gz │ ├── rsids-v150-hg38.tsv.gz │ ├── rsids-v154-hg19.tsv.gz │ └── rsids-v154-hg38.tsv.gz └── phenolist │ ├── phenolist-example-broken.csv │ └── phenolist-example1.csv ├── run-all.sh ├── run-gunicorn.sh ├── test_all.py ├── test_detectref.py ├── 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