├── .gitignore ├── .jshintrc ├── .travis.yml ├── API.md ├── CHANGELOG.md ├── CONTRIBUTING.md ├── DEVELOP.md ├── ENVTEMPLATE.sh ├── LICENSE ├── Makefile ├── README.md ├── alembic.ini ├── alembic ├── env.py ├── script.py.mako └── versions │ ├── .keep │ ├── 1ab5aa1e3054_start_associating_comments_with_.py │ ├── 2c00861f3ff1_vcfs_store_inferred_ensembl_release.py │ └── 46fbcb9e7ce5_add_the_starred_annotation_to_genotypes.py ├── common ├── __init__.py ├── helpers.py └── relational_vcf.py ├── config.py ├── cycledash ├── __init__.py ├── api │ ├── __init__.py │ ├── bams.py │ ├── comments.py │ ├── ga4gh_wrapper.py │ ├── genotypes.py │ ├── projects.py │ ├── runs.py │ └── tasks.py ├── auth.py ├── helpers.py ├── static │ ├── img │ │ ├── cycle-dash.png │ │ ├── favicon.ico │ │ ├── igv32x32.jpg │ │ ├── loader.gif │ │ └── subtle-dots.png │ ├── js │ │ ├── CompletionUtils.js │ │ ├── QueryCompletion.js │ │ ├── QueryLanguage.js │ │ ├── comments │ │ │ ├── comments.js │ │ │ └── components │ │ │ │ └── comment.js │ │ ├── examine │ │ │ ├── Dispatcher.js │ │ │ ├── RecordActions.js │ │ │ ├── RecordStore.js │ │ │ ├── components │ │ │ │ ├── CommentBox.js │ │ │ │ ├── Downloads.js │ │ │ │ ├── ExamineInformation.js │ │ │ │ ├── ExaminePage.js │ │ │ │ ├── PileupViewer.js │ │ │ │ ├── QueryBox.js │ │ │ │ ├── RecordsShown.js │ │ │ │ ├── StatsSummary.js │ │ │ │ ├── VCFTable.js │ │ │ │ ├── VCFValidation.js │ │ │ │ └── types.js │ │ │ ├── examine.js │ │ │ └── utils.js │ │ └── runs │ │ │ ├── components │ │ │ ├── RunsPage.js │ │ │ └── forms.js │ │ │ └── runs.js │ └── scss │ │ ├── _variables.scss │ │ ├── examine.scss │ │ ├── header.scss │ │ ├── runs.scss │ │ └── style.scss ├── templates │ ├── about.html │ ├── comments.html │ ├── examine.html │ ├── layouts │ │ └── layout.html │ ├── login.html │ ├── macros │ │ ├── flash.html │ │ └── nav.html │ ├── register.html │ ├── runs.html │ └── tasks.html ├── validations.py └── views.py ├── grammars └── querylanguage.pegjs ├── gulpfile.js ├── licenses ├── APACHE-LICENSE-2.0.txt ├── CREATIVE-COMMONS-BY-3.0.txt └── CREATIVE-COMMONS-BY-4.0.txt ├── package.json ├── readme-screenshot.png ├── requirements.txt ├── run.py ├── run.sh ├── schema.py ├── scripts ├── changelog.py ├── generate-coverage-report.sh ├── init_db.py ├── lint.sh ├── release │ └── README.md ├── run-js-tests.sh ├── run-python-tests.sh ├── seltest-remote-capabilities.json ├── start-worker.sh ├── travis-coverage.sh ├── travis-run-pdiff-tests.sh ├── travis-setup.sh ├── travis-test.sh ├── update-screenshots.sh ├── upgrade.sh └── xml_to_lcov.py ├── tests ├── ENV.sh ├── create-test-db.sh ├── data.sql ├── data │ ├── comment-db.json │ ├── diverse.nochr.vcf │ ├── diverse.vcf │ ├── one-sample.vcf │ ├── snv.truth.vcf │ ├── snv.vcf │ ├── somatic_hg19_14muts.vcf │ └── validation.vcf ├── js │ ├── CommentUtils.js │ ├── CompletionUtils-test.js │ ├── DataUtils-test.js │ ├── DataUtils.js │ ├── ExaminePage-comments-test.js │ ├── ExaminePage-test.js │ ├── IGVLink-test.js │ ├── Utils-test.js │ ├── Utils.js │ ├── blanket-stub-jsx.js │ ├── examine-utils-test.js │ ├── jsx-stub-transformer.js │ ├── preprocessor.js │ ├── query-completion-test.js │ ├── query-test.js │ └── testdom.js ├── pdifftests │ ├── README.md │ ├── images │ │ ├── examine_bad-query.png │ │ ├── examine_base.png │ │ ├── examine_comments-edit.png │ │ ├── examine_comments-view.png │ │ ├── examine_filter.png │ │ ├── examine_sorted.png │ │ ├── examine_tooltip.png │ │ ├── examine_validation.png │ │ ├── runs_add-bam.png │ │ ├── runs_add-run.png │ │ ├── runs_bams.png │ │ ├── runs_info.png │ │ ├── runs_new-project.png │ │ ├── runs_no-bams.png │ │ ├── runs_page.png │ │ ├── tasks_page.png │ │ ├── website_about-page.png │ │ ├── website_comments.png │ │ ├── website_login.png │ │ └── website_register.png │ └── test.py ├── playground │ ├── require.js │ └── typeahead.html ├── python │ ├── helpers.py │ ├── test.py │ ├── test_authentication.py │ ├── test_bams_api.py │ ├── test_comments_api.py │ ├── test_download.py │ ├── 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