From f116548d7e88b82eaf6dac8588490aa659a89761 Mon Sep 17 00:00:00 2001 From: Dario Beraldi Date: Mon, 25 Sep 2023 23:45:14 +0100 Subject: [PATCH] Add e2e testing with Cypress (#283) * Start adding some cypress tests * Start adding some cypress tests * Add tests and refactor * Start adding some cypress tests * Add tests and refactor * Start adding some cypress tests * Several edit to cypress tests * Work in progress mostly on feature resizing * Remove old test files * Test cypress-mongodb * Lower packageExtensions bson version * Replace mongosh with cypress-mongo * Fix linter * Minor tidying up * Start adding some cypress tests * Add tests and refactor * Start adding some cypress tests * Several edit to cypress tests * Work in progress mostly on feature resizing * Start adding some cypress tests * Add tests and refactor * Start adding some cypress tests * Remove old test files * Test cypress-mongodb * Lower packageExtensions bson version * Replace mongosh with cypress-mongo * Fix linter * Minor tidying up * Edits tests and add workflow * Update script; Fix linter * Minor edits to variable names * Try setting viewport size; Fix assembly name * Set viewport in config; Set log level and trigger in workflow * Tweaks to tests. Add downloads to gitignore * Simplify grep * Add test:ci * Replace system call with cypress/ts code. Wait for download * Remove unsused import * Allow retries to reduce false alarms (not ideal) * Merge feature with end coordinate fixed * Edit relevant test * Add new test * Fix test by simplifing input file and increase waiting * Small cleanups * Update Cypress file linting * Rearrange tests a bit --------- Co-authored-by: Garrett Stevens --- .eslintrc.js | 52 +- .github/workflows/cypress_debug.yml | 42 + .github/workflows/pull_request.yml | 17 +- .yarnrc.yml | 3 + .../apollo-collaboration-server/package.json | 3 +- packages/jbrowse-plugin-apollo/.gitignore | 1 + packages/jbrowse-plugin-apollo/README.md | 62 + .../jbrowse-plugin-apollo/cypress.config.js | 37 +- .../cypress/e2e/addAssembly.cy.ts | 46 + .../cypress/e2e/apollo.cy.ts | 16 - .../cypress/e2e/downloadGff.cy.ts | 40 + .../cypress/e2e/editFeature.cy.ts | 131 ++ .../cypress/e2e/jbrowse.cy.ts | 11 - .../cypress/e2e/searchFeatures.cy.ts | 51 + .../cypress/fixtures/config.json | 51 - .../cypress/support/commands.ts | 94 +- .../cypress/support/e2e.ts | 9 + .../cypress/support/index.d.ts | 17 + .../cypress/tsconfig.json | 5 +- packages/jbrowse-plugin-apollo/package.json | 10 +- .../components/LinearApolloDisplay.tsx | 3 + .../test_data/onegene.fasta.gff3 | 25 + .../test_data/space.gff3 | 905 +++++++++++++ .../jbrowse-plugin-apollo/test_data/volvox.fa | 897 +++++++++++++ .../test_data/volvox.fasta.gff3 | 1144 +++++++++++++++++ .../test_data/volvox2.fasta.gff3 | 906 +++++++++++++ .../tsconfig.eslint.json | 2 +- yarn.lock | 77 +- 28 files changed, 4485 insertions(+), 172 deletions(-) create mode 100644 .github/workflows/cypress_debug.yml create mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/addAssembly.cy.ts delete mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/apollo.cy.ts create mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/downloadGff.cy.ts create mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts delete mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/jbrowse.cy.ts create mode 100644 packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts delete mode 100644 packages/jbrowse-plugin-apollo/cypress/fixtures/config.json create mode 100644 packages/jbrowse-plugin-apollo/cypress/support/index.d.ts create mode 100644 packages/jbrowse-plugin-apollo/test_data/onegene.fasta.gff3 create mode 100644 packages/jbrowse-plugin-apollo/test_data/space.gff3 create mode 100644 packages/jbrowse-plugin-apollo/test_data/volvox.fa create mode 100644 packages/jbrowse-plugin-apollo/test_data/volvox.fasta.gff3 create mode 100644 packages/jbrowse-plugin-apollo/test_data/volvox2.fasta.gff3 diff --git a/.eslintrc.js b/.eslintrc.js index 2865cf979..67cff678e 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -113,7 +113,7 @@ module.exports = { ], }, }, - // Lint non-src files (e.g. jest.config.js) using a separate tsconfig + // Lint non-src JS files (e.g. jest.config.js) using a separate tsconfig { files: ['./packages/jbrowse-plugin-apollo/*.js'], parserOptions: { @@ -121,55 +121,17 @@ module.exports = { }, env: { node: true }, }, - // Specify Node env for cypress testing files + // Specify Node env and tsconfig for cypress testing and config files { - files: ['./packages/jbrowse-plugin-apollo/cypress/**/*.js'], - env: { node: true }, - }, - // Specify Node env for apollo-collaboration-server/ - { - files: ['./packages/apollo-collaboration-server/**/*.ts'], - env: { node: true }, - }, - // Don't enforce tsdoc syntax in JS files - { - files: ['./packages/jbrowse-plugin-apollo/**/*.{ts,tsx}'], - env: { browser: true }, - extends: [ - 'plugin:react/recommended', - 'plugin:react-hooks/recommended', - 'plugin:jsx-a11y/recommended', + files: [ + './packages/jbrowse-plugin-apollo/cypress.config.js', + './packages/jbrowse-plugin-apollo/cypress/**/*.{j,t}s', ], - settings: { - // These settings are from eslint-plugin-react - react: { - // React version. "detect" automatically picks the version you have installed. - // You can also use `16.0`, `16.3`, etc, if you want to override the detected value. - // It will default to "latest" and warn if missing, and to "detect" in the future - version: 'detect', - }, - componentWrapperFunctions: [ - // The name of any function used to wrap components, e.g. Mobx `observer` function. If this isn't set, components wrapped by these functions will be skipped. - 'observer', // `property` - { property: 'styled' }, // `object` is optional - { property: 'observer', object: 'Mobx' }, - { property: 'observer', object: '' }, // sets `object` to whatever value `settings.react.pragma` is set to - ], - }, - }, - // Lint non-src files (e.g. jest.config.js) using a separate tsconfig - { - files: ['./packages/jbrowse-plugin-apollo/*.js'], parserOptions: { - project: 'packages/jbrowse-plugin-apollo/tsconfig.eslint.json', + project: 'packages/jbrowse-plugin-apollo/cypress/tsconfig.json', }, env: { node: true }, }, - // Specify Node env for cypress testing files - { - files: ['./packages/jbrowse-plugin-apollo/cypress/**/*.js'], - env: { node: true }, - }, // Specify Node env for apollo-collaboration-server/ { files: ['./packages/apollo-collaboration-server/**/*.ts'], @@ -183,4 +145,4 @@ module.exports = { }, }, ], -}; +} diff --git a/.github/workflows/cypress_debug.yml b/.github/workflows/cypress_debug.yml new file mode 100644 index 000000000..2bae6078b --- /dev/null +++ b/.github/workflows/cypress_debug.yml @@ -0,0 +1,42 @@ +name: Cypress debug +on: workflow_dispatch + +jobs: + build: + name: End-to-end test + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Use Node.js 18.x + uses: actions/setup-node@v3 + with: + node-version: 18 + cache: yarn + + - name: Install + run: yarn --immutable + + - name: Get latest JBrowse + working-directory: packages/jbrowse-plugin-apollo + run: yarn run jbrowse create --nightly .jbrowse + + - name: Start MongoDB + uses: supercharge/mongodb-github-action@1.10.0 + with: + mongodb-version: 7 + mongodb-replica-set: test-rs + + - name: Run tests + working-directory: packages/jbrowse-plugin-apollo + env: + GUEST_USER_ROLE: admin + MONGODB_URI: mongodb://localhost:27017/apolloTestDb + LOG_LEVELS: error,warn,log + run: yarn run test:e2e:debug + + - name: Archive test results + if: '!cancelled()' + uses: actions/upload-artifact@v3 + with: + name: cypress_results + path: packages/jbrowse-plugin-apollo/cypress diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index cb5083385..684bcdca4 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -23,8 +23,23 @@ jobs: working-directory: packages/apollo-shared - name: Lint codebase run: yarn eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx . - - name: Test codebase + - name: Run Jest tests run: yarn test + - name: Get latest JBrowse + working-directory: packages/jbrowse-plugin-apollo + run: yarn run jbrowse create --nightly .jbrowse + - name: Start MongoDB + uses: supercharge/mongodb-github-action@1.10.0 + with: + mongodb-version: 7 + mongodb-replica-set: test-rs + - name: Run Cypress tests + working-directory: packages/jbrowse-plugin-apollo + env: + GUEST_USER_ROLE: admin + MONGODB_URI: mongodb://localhost:27017/apolloTestDb + LOG_LEVELS: error,warn,log + run: yarn run test:e2e - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v3 env: diff --git a/.yarnrc.yml b/.yarnrc.yml index 5fe53e835..f078f2b82 100644 --- a/.yarnrc.yml +++ b/.yarnrc.yml @@ -7,6 +7,9 @@ packageExtensions: dependencies: "#ansi-styles": "npm:ansi-styles@6.1.0" "#supports-color": "npm:supports-color@9.2.2" + cypress-mongodb@*: + dependencies: + bson: "^4" material-ui-popup-state@*: peerDependencies: "@emotion/react": "*" diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index 836b0a1bc..03805f4a7 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -20,7 +20,8 @@ "test:watch": "jest --watch", "test:cov": "jest --coverage", "test:debug": "node --inspect-brk -r tsconfig-paths/register -r ts-node/register node_modules/.bin/jest --runInBand", - "test:e2e": "jest --config ./test/jest-e2e.json" + "test:e2e": "jest --config ./test/jest-e2e.json", + "cypress:start": "GUEST_USER_ROLE=admin MONGODB_URI=mongodb://localhost:27017/apolloTestDb yarn start" }, "dependencies": { "@emotion/react": "^11.10.6", diff --git a/packages/jbrowse-plugin-apollo/.gitignore b/packages/jbrowse-plugin-apollo/.gitignore index fb83311cd..a317d4aea 100644 --- a/packages/jbrowse-plugin-apollo/.gitignore +++ b/packages/jbrowse-plugin-apollo/.gitignore @@ -3,3 +3,4 @@ # Cypress specific files cypress/videos cypress/screenshots +cypress/downloads diff --git a/packages/jbrowse-plugin-apollo/README.md b/packages/jbrowse-plugin-apollo/README.md index c9ce48a7c..9db65d286 100644 --- a/packages/jbrowse-plugin-apollo/README.md +++ b/packages/jbrowse-plugin-apollo/README.md @@ -1 +1,63 @@ # jbrowse-plugin-apollo + +## Testing with cypress + +These notes setup cypress and run tests. These notes are likely to change. + +- One time step: **Outside** the Apollo dev container + [install cypress](https://docs.cypress.io/guides/getting-started/installing-cypress). + E.g. on your OS terminal (not vscode) run: + +``` +yarn --cwd packages/jbrowse-plugin-apollo add cypress --dev +yarn --cwd packages/jbrowse-plugin-apollo add cypress-mongodb --dev +``` + +Add these lines to the `packageExtensions` section of `.yarnrc.yml`: + +``` + cypress-mongodb@*: + dependencies: + bson: "*" +``` + +Then run `yarn` again. + +--- + +- Start [jbrowse](https://github.com/GMOD/jbrowse-components): You may want to + pull the latest code to be consistent with the GitHub workflow + +``` +cd /path/to/jbrowse-components +git pull +yarn --cwd products/jbrowse-web start +``` + +- Start Apollo server. Within the docker container (_i.e_ within vscode) and in + distinct terminals run: + +``` +yarn --cwd packages/apollo-shared start +``` + +``` +yarn --cwd packages/apollo-collaboration-server run cypress:start +``` + +``` +yarn --cwd packages/jbrowse-plugin-apollo start +``` + +If above you change the name fo the test database (`apolloTestDb`), change +accordingly in `commands.ts` + +- Open cypress in the testing directory, _i.e._ where yo have the relevant + `package.json`. Typically (again outside the dev container/vscode): + +``` +yarn --cwd packages/jbrowse-plugin-apollo run cypress open +``` + +- For end-to-end testing, click "E2E Testing" `->` Chrome `->` + `Start E2E Testing`. Click on one of the available test scripts. diff --git a/packages/jbrowse-plugin-apollo/cypress.config.js b/packages/jbrowse-plugin-apollo/cypress.config.js index 3b58d326c..5ceb8cd53 100644 --- a/packages/jbrowse-plugin-apollo/cypress.config.js +++ b/packages/jbrowse-plugin-apollo/cypress.config.js @@ -1,7 +1,36 @@ -module.exports = { +// eslint-disable-next-line @typescript-eslint/no-var-requires +const { defineConfig } = require('cypress') +// eslint-disable-next-line @typescript-eslint/no-var-requires +const { configurePlugin } = require('cypress-mongodb') +// eslint-disable-next-line @typescript-eslint/no-var-requires +const fs = require('node:fs') + +module.exports = defineConfig({ + // Make viewport long and thin to avoid the scrollbar on the right intefere + // with the coordinates + viewportHeight: 2000, + viewportWidth: 1000, + retries: { + runMode: 2, + }, + env: { + mongodb: { + uri: 'mongodb://localhost:27017/?directConnection=true', + database: 'apolloTestDb', + }, + }, + screenshotOnRunFailure: false, + video: false, e2e: { - setupNodeEvents(_on, _config) { - // implement node event listeners here + baseUrl: 'http://localhost:8999', + setupNodeEvents(on, config) { + configurePlugin(on) + on('task', { + readdirSync(path) { + return fs.readdirSync(path) + }, + }) + return config }, }, -} +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/addAssembly.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/addAssembly.cy.ts new file mode 100644 index 000000000..d6806b144 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/addAssembly.cy.ts @@ -0,0 +1,46 @@ +describe('Add Assembly', () => { + beforeEach(() => { + cy.deleteAssemblies() + cy.loginAsGuest() + }) + + it('Can add assembly from fasta', () => { + cy.contains('Apollo').click() + cy.contains('Add Assembly').click() + cy.get('input[type="TextField"]').type('volvox_deleteme') + cy.get('input[value="text/x-fasta"]').check() + cy.get('input[type="file"]').selectFile('test_data/volvox.fa') + + cy.intercept('/changes').as('changes') + cy.contains('Submit').click() + cy.contains('is being added', { timeout: 10_000 }) + cy.wait('@changes').its('response.statusCode').should('match', /2../) + }) + + it('Can add assembly from gff3 with fasta', () => { + cy.contains('Apollo').click() + cy.contains('Add Assembly').click() + cy.get('input[type="TextField"]').type('volvox_deleteme') + cy.get('input[value="text/x-gff3"]').check() + cy.get('input[type="file"]').selectFile('test_data/volvox.fasta.gff3') + + cy.intercept('/changes').as('changes') + cy.contains('Submit').click() + cy.contains('is being added', { timeout: 10_000 }) + cy.wait('@changes').its('response.statusCode').should('match', /2../) + }) + + it('FIXME: Can add assembly from 2bit', () => { + cy.contains('Apollo').click() + cy.contains('Add Assembly').click() + cy.get('input[type="TextField"]').type('volvox_deleteme') + cy.get('input[value="text/x-fasta"]').check() + cy.get('input[type="file"]').selectFile('test_data/volvox.2bit') + + cy.intercept('/changes').as('changes') + cy.contains('Submit').click() + cy.contains('is being added', { timeout: 10_000 }) + // Should match /2../ instead + cy.wait('@changes').its('response.statusCode').should('match', /4../) + }) +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/apollo.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/apollo.cy.ts deleted file mode 100644 index bda5c1169..000000000 --- a/packages/jbrowse-plugin-apollo/cypress/e2e/apollo.cy.ts +++ /dev/null @@ -1,16 +0,0 @@ -describe('My First Test', () => { - it('visits JBrowse with Apollo', () => { - // You can put JBrowse 2 into any session you want this way at the beginning - // of your test! - cy.fixture('apollo_view.json').then((sessionData) => { - cy.writeFile( - '.jbrowse/apollo_view.json', - JSON.stringify(sessionData, null, 2), - ) - cy.visit('/?config=apollo_view.json') - - // The plugin successfully loads - cy.contains('Log in to Demo Server') - }) - }) -}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/downloadGff.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/downloadGff.cy.ts new file mode 100644 index 000000000..de2c84766 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/downloadGff.cy.ts @@ -0,0 +1,40 @@ +describe('Download GFF', () => { + beforeEach(() => { + cy.exec(`rm ${Cypress.config('downloadsFolder')}/*_apollo.gff3`, { + failOnNonZeroExit: false, + }).then((result) => { + cy.log(result.stderr) + }) + cy.deleteAssemblies() + cy.loginAsGuest() + }) + + it('Can download gff', () => { + cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3') + cy.get('button[data-testid="dropDownMenuButton"]') + .contains('Apollo') + .click() + cy.contains('Download GFF3').click() + cy.focused() + .contains('Select assembly') + .parent() + .within(() => { + cy.get('input').parent().click() + }) + cy.contains('volvox.fasta.gff3').click() + cy.get('button').contains('Download').click() + + // We don't know when the download is done + // eslint-disable-next-line cypress/no-unnecessary-waiting + cy.wait(4000) + cy.task('readdirSync', Cypress.config('downloadsFolder')).then((out) => { + const gff = out as string + cy.readFile(`${Cypress.config('downloadsFolder')}/${gff[0]}`).then( + (x: string) => { + const lines: string[] = x.trim().split('\n') + expect(lines.length).eq(247) + }, + ) + }) + }) +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts new file mode 100644 index 000000000..2cd3b8d16 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts @@ -0,0 +1,131 @@ +describe('Different ways of editing features', () => { + beforeEach(() => { + cy.deleteAssemblies() + cy.loginAsGuest() + }) + + it('Edit feature via table editor', () => { + const assemblyName = 'space.gff3' + cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`) + cy.selectAssemblyToView(assemblyName) + + cy.contains('Open track selector').click() + cy.contains('Annotations (').click() + cy.get('[data-testid="MinimizeIcon"]').eq(1).click() + cy.contains('Drawer minimized') + .parent() + .within(() => { + cy.get('[data-testid="CloseIcon"]').click() + }) + + cy.contains('Table') + .parent() + .within(() => { + cy.get('[data-testid]').then((el) => { + const expandIcon: string = el.attr('data-testid') ?? '' + if (expandIcon == 'ExpandLessIcon') { + cy.log('Expanded') + } else if (expandIcon == 'ExpandMoreIcon') { + cy.contains('Table').click() + } else { + cy.log(`Unexpected value for expand icon: ${expandIcon}`) + } + }) + }) + + cy.get('input[placeholder="Search for location"]').type( + 'ctgA:9400..9600{enter}', + ) + + cy.get('tbody', { timeout: 10_000 }) + .contains('tr', 'Match5') + .within(() => { + cy.get('input[type="text"][value="EST_match"]').type('CDS{enter}', { + force: true, + }) + cy.contains('td', '9520').within(() => { + cy.get('input').type('{selectall}{backspace}9432') + }) + cy.contains('td', '9900').within(() => { + cy.get('input').type('{selectall}{backspace}9567') + }) + }) + cy.get('body').click(0, 0) + + // Check edit is done + cy.reload() + cy.get('tbody', { timeout: 10_000 }).within(() => { + cy.get('input[type="text"][value="CDS"]') + cy.contains('9432') + cy.contains('9567') + }) + }) + + it('Suggest only valid SO terms from dropdown', () => { + cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3') + cy.selectAssemblyToView('onegene.fasta.gff3') + cy.searchFeatures('gx1') + // In headless mode it seems to take a long time for menus to be populated + cy.get('input[type="text"][value="exon"]', { timeout: 60_000 }) + .eq(0) + .click({ timeout: 60_000, force: true }) + cy.contains('li', /^CDS$/, { timeout: 60_000, matchCase: false }).should( + 'exist', + ) + cy.contains('li', /^gene$/, { timeout: 60_000, matchCase: false }).should( + 'not.exist', + ) + }) + + it.skip('Can select region on rubber-band and zoom into it', () => { + const assemblyName = 'space.gff3' + cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`) + cy.selectAssemblyToView(assemblyName) + cy.get('input[placeholder="Search for location"]').type( + 'ctgA:1..10000{enter}', + ) + cy.get('[data-testid="rubberband_controls"]').trigger('mouseover') + cy.get('[data-testid="rubberband_controls"]').trigger('mousedown', 100, 5) + cy.get('[data-testid="rubberband_controls"]').trigger('mousemove', 200, 5) + cy.get('[data-testid="rubberband_controls"]').trigger('mouseup', 200, 5, { + force: true, + }) + cy.intercept('POST', '/users/userLocation').as('done') + cy.contains('Zoom to region').click() + cy.wait('@done') + cy.currentLocationEquals('ctgA', 1021, 2041, 10) + }) + + it.skip('Can drag and move position', () => { + const assemblyName = 'space.gff3' + cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`) + cy.selectAssemblyToView(assemblyName) + cy.contains('Open track selector').click() + cy.contains('Annotations (').click() + cy.get('[data-testid="MinimizeIcon"]').eq(1).click() + cy.get('input[placeholder="Search for location"]').type( + 'ctgA:9400..9600{enter}', + ) + // cy.contains('Table').click() + // cy.contains('Match5').click() + // cy.get('[data-testid="MoreVertIcon"]').click() + // cy.contains('Minimize track').click() + // cy.get('[data-testid="MoreVertIcon"]').click() + // cy.contains('Restore track').click() + + cy.get('[data-testid="overlayCanvas"]').then((canvas) => { + cy.wrap(canvas).trigger('mouseover', 700, 10) // .rightclick() + }) + // cy.get('[class="css-17gfnt3-verticalGuidesContainer"]').children().eq(0).trigger('mousedown', 200, 30) + // cy.get('[class="css-17gfnt3-verticalGuidesContainer"]').children().eq(0).trigger('mousemove', 900, 30) + // cy.get('[class="css-17gfnt3-verticalGuidesContainer"]').children().eq(0).trigger('mouseup', 900, 30) + + // cy.get('[data-testid="trackContainer"]').children().eq(0).children().trigger('mousedown', 700, 30, { force: true }) + // cy.get('[data-testid="trackContainer"]').children().eq(0).children().trigger('mousemove', 900, 30, { force: true }) + // cy.get('[data-testid="trackContainer"]').children().eq(0).children().trigger('mouseup', 900, 30, { force: true }) + // .parent().parent().trigger('mouseover') + // cy.get('[data-testid="canvas"]').parent().parent().trigger('mousedown', 580, 30) + // cy.get('[data-testid="canvas"]').parent().parent().trigger('mousemove', 200, 30) + // cy.get('[data-testid="canvas"]').parent().parent().trigger('mouseup', 200, 30) + }) +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/jbrowse.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/jbrowse.cy.ts deleted file mode 100644 index c70f8e89a..000000000 --- a/packages/jbrowse-plugin-apollo/cypress/e2e/jbrowse.cy.ts +++ /dev/null @@ -1,11 +0,0 @@ -describe('My First Test', () => { - it('visits JBrowse', () => { - cy.fixture('config.json').then((sessionData) => { - cy.writeFile('.jbrowse/config.json', JSON.stringify(sessionData, null, 2)) - cy.visit('/') - - // The plugin successfully loads - cy.contains('Select assembly to view') - }) - }) -}) diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts new file mode 100644 index 000000000..97e230671 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts @@ -0,0 +1,51 @@ +describe('Search features', () => { + beforeEach(() => { + cy.deleteAssemblies() + cy.loginAsGuest() + }) + + it('One hit, no children', () => { + cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3') + cy.selectAssemblyToView('volvox.fasta.gff3') + cy.searchFeatures('Match6') + cy.currentLocationEquals('ctgA', 8000, 9000, 10) + }) + + it('One matching Parent and multiple matching children', () => { + cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3') + cy.selectAssemblyToView('volvox.fasta.gff3') + cy.searchFeatures('EDEN') + cy.currentLocationEquals('ctgA', 1050, 9000, 10) + }) + + it('Search only the selected assembly', () => { + cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3') + cy.addAssemblyFromGff('volvox2.fasta.gff3', 'test_data/volvox2.fasta.gff3') + + cy.selectAssemblyToView('volvox2.fasta.gff3') + cy.searchFeatures('SpamGene') + cy.currentLocationEquals('ctgA', 100, 200, 10) + + cy.visit('/?config=http://localhost:9000/jbrowse_config.json') + cy.selectAssemblyToView('volvox.fasta.gff3') + cy.searchFeatures('SpamGene') + cy.contains('Error: Unknown reference sequence "SpamGene"') + }) + + it('Can use quotes to handle spaces', () => { + cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3') + cy.selectAssemblyToView('space.gff3') + cy.searchFeatures('"agt A"') + cy.currentLocationEquals('ctgA', 7500, 8000, 10) + }) + + it('FIXME: Can handle regex and space in attribute values', () => { + cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3') + cy.selectAssemblyToView('space.gff3') + cy.get('input[placeholder="Search for location"]').type('Ma*.1{enter}') + cy.contains('Search results') + // It should instead either: + // * Return only one hit for Match1, or + // * Return 'Error: Unknown reference sequence' + }) +}) diff --git a/packages/jbrowse-plugin-apollo/cypress/fixtures/config.json b/packages/jbrowse-plugin-apollo/cypress/fixtures/config.json deleted file mode 100644 index 906c4f73f..000000000 --- a/packages/jbrowse-plugin-apollo/cypress/fixtures/config.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "assemblies": [ - { - "name": "volvox", - "aliases": [ - "vvx" - ], - "sequence": { - "type": "ReferenceSequenceTrack", - "trackId": "volvox_refseq", - "adapter": { - "type": "TwoBitAdapter", - "twoBitLocation": { - "uri": "test_data/volvox/volvox.2bit" - } - } - }, - "refNameAliases": { - "adapter": { - "type": "FromConfigAdapter", - "features": [ - { - "refName": "ctgA", - "uniqueId": "alias1", - "aliases": [ - "A", - "contigA" - ] - }, - { - "refName": "ctgB", - "uniqueId": "alias2", - "aliases": [ - "B", - "contigB" - ] - } - ] - } - } - } - ], - "defaultSession": { - "name": "New session", - "views": [ - { - "type": "LinearGenomeView" - } - ] - } -} diff --git a/packages/jbrowse-plugin-apollo/cypress/support/commands.ts b/packages/jbrowse-plugin-apollo/cypress/support/commands.ts index 119ab03f7..9b46c1eb1 100644 --- a/packages/jbrowse-plugin-apollo/cypress/support/commands.ts +++ b/packages/jbrowse-plugin-apollo/cypress/support/commands.ts @@ -1,25 +1,69 @@ -// *********************************************** -// This example commands.js shows you how to -// create various custom commands and overwrite -// existing commands. -// -// For more comprehensive examples of custom -// commands please read more here: -// https://on.cypress.io/custom-commands -// *********************************************** -// -// -// -- This is a parent command -- -// Cypress.Commands.add('login', (email, password) => { ... }) -// -// -// -- This is a child command -- -// Cypress.Commands.add('drag', { prevSubject: 'element'}, (subject, options) => { ... }) -// -// -// -- This is a dual command -- -// Cypress.Commands.add('dismiss', { prevSubject: 'optional'}, (subject, options) => { ... }) -// -// -// -- This will overwrite an existing command -- -// Cypress.Commands.overwrite('visit', (originalFn, url, options) => { ... }) +Cypress.Commands.add('loginAsGuest', () => { + cy.visit('/?config=http://localhost:9000/jbrowse_config.json') + cy.contains('Continue as Guest', { timeout: 10_000 }).click() + // eslint-disable-next-line cypress/no-unnecessary-waiting + cy.wait(2000) + cy.reload() +}) + +Cypress.Commands.add('deleteAssemblies', () => { + for (const x of ['assemblies', 'features']) { + cy.log(x) + cy.deleteMany({}, { collection: x }).then((results: undefined) => { + cy.log(`Collection ${x}: ${results}` as unknown as string) + }) + } +}) + +Cypress.Commands.add('addAssemblyFromGff', (assemblyName, fin) => { + cy.get('button[data-testid="dropDownMenuButton"]', { timeout: 10_000 }) + .contains('Apollo') + .click({ force: true, timeout: 10_000 }) + cy.contains('Add Assembly', { timeout: 10_000 }).click() + cy.get('input[type="TextField"]').type(assemblyName) + cy.get('input[value="text/x-gff3"]').check() + cy.get('input[type="file"]').selectFile(fin) + cy.get('[data-testid="CheckBoxIcon"]') + .parent() + .children() + .get('input[type="checkbox"]') + .should('be.checked') + cy.intercept('/changes').as('changes') + cy.contains('Submit').click() + cy.wait('@changes').its('response.statusCode').should('match', /2../) + cy.reload() + cy.contains('Select assembly to view', { timeout: 10_000 }) +}) + +Cypress.Commands.add('selectAssemblyToView', (assemblyName) => { + cy.contains('Select assembly to view', { timeout: 10_000 }) + cy.get('input[data-testid="assembly-selector"]').parent().click() + cy.contains(assemblyName).parent().click() + cy.intercept('POST', '/users/userLocation').as('selectAssemblyToViewDone') + cy.contains('Open').click() + cy.wait('@selectAssemblyToViewDone') +}) + +Cypress.Commands.add('searchFeatures', (query) => { + cy.intercept('POST', '/users/userLocation').as('searchFeaturesDone') + cy.get('input[placeholder="Search for location"]').type(`${query}{enter}`) + cy.wait('@searchFeaturesDone') +}) + +Cypress.Commands.add( + 'currentLocationEquals', + (contig, start, end, tolerance) => { + cy.get('input[placeholder="Search for location"]') + .invoke('val') + .as('currentLocation') + + cy.get('@currentLocation').then((currentLocation) => { + const [xcontig, s, e] = currentLocation.split(/:|\.\./) + const xstart: number = Number.parseInt(s.replace(',', ''), 10) + const xend: number = Number.parseInt(e.replace(',', ''), 10) + expect(xcontig).equal(contig) + expect(xstart).to.be.within(start - tolerance, end + tolerance) + expect(xend).to.be.within(end - tolerance, end + tolerance) + }) + }, +) diff --git a/packages/jbrowse-plugin-apollo/cypress/support/e2e.ts b/packages/jbrowse-plugin-apollo/cypress/support/e2e.ts index d1dd1353e..ca6404218 100644 --- a/packages/jbrowse-plugin-apollo/cypress/support/e2e.ts +++ b/packages/jbrowse-plugin-apollo/cypress/support/e2e.ts @@ -18,3 +18,12 @@ import './commands' // Alternatively you can use CommonJS syntax: // require('./commands') +import { addCommands } from 'cypress-mongodb/dist/index-browser' + +addCommands() + +// Cypress.on('uncaught:exception', (err, _runnable) => { +// if (err.message.includes('ResizeObserver')) { +// return false +// } +// }) diff --git a/packages/jbrowse-plugin-apollo/cypress/support/index.d.ts b/packages/jbrowse-plugin-apollo/cypress/support/index.d.ts new file mode 100644 index 000000000..00d58cf02 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/cypress/support/index.d.ts @@ -0,0 +1,17 @@ +/// + +declare namespace Cypress { + interface Chainable { + loginAsGuest(): Chainable + deleteAssemblies(): Chainable + addAssemblyFromGff(assemblyName: string, fin: string): Chainable + selectAssemblyToView(assemblyName: string): Chainable + searchFeatures(query: string): Chainable + currentLocationEquals( + contig: string, + start: number, + end: number, + tolerance: number, + ): Chainable + } +} diff --git a/packages/jbrowse-plugin-apollo/cypress/tsconfig.json b/packages/jbrowse-plugin-apollo/cypress/tsconfig.json index 4c1f30330..8e657f2f3 100644 --- a/packages/jbrowse-plugin-apollo/cypress/tsconfig.json +++ b/packages/jbrowse-plugin-apollo/cypress/tsconfig.json @@ -5,5 +5,8 @@ "types": ["cypress", "node"], "strict": true, }, - "include": ["**/*.ts"] + "include": [ + "**/*.ts", + "../cypress.config.js" + ] } diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index 160fed2e3..e460a9281 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -37,9 +37,12 @@ "browse": "serve --listen 8999 .jbrowse", "test": "jest", "test:ci": "jest --coverage", - "test:e2e": "start-test \"npm-run-all --parallel start browse\" \"9000|8999\" \"npm-run-all cypress:run\"", - "cypress:run": "cypress run --browser chrome --config baseUrl=http://localhost:8999", - "cypress:open": "cypress open --config baseUrl=http://localhost:8999", + "start:collab": "yarn workspace apollo-collaboration-server run start", + "test:e2e": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:run\"", + "test:e2e:debug": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:debug\"", + "cypress:run": "cypress run --browser chrome", + "cypress:debug": "cypress run --browser chrome --config screenshotOnRunFailure=true,video=true", + "cypress:open": "cypress open --config baseUrl=http://localhost:3000", "prepublish": "yarn test", "prepack": "yarn build", "postversion": "git push --follow-tags" @@ -98,6 +101,7 @@ "@types/react": "^17.0.34", "@types/react-dom": "^18", "cypress": "^12.17.2", + "cypress-mongodb": "^6.2.0", "fake-indexeddb": "^4.0.2", "jest": "^29.6.2", "jest-fetch-mock": "^3.0.3", diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx index 6f7b246d4..1d129d14a 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx @@ -93,6 +93,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay( width={lgv.dynamicBlocks.totalWidthPx} height={featuresHeight} className={classes.canvas} + data-testid="collaboratorCanvas" /> { @@ -102,6 +103,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay( width={lgv.dynamicBlocks.totalWidthPx} height={featuresHeight} className={classes.canvas} + data-testid="canvas" /> { @@ -119,6 +121,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay( }} className={classes.canvas} style={{ cursor: cursor ?? 'default' }} + data-testid="overlayCanvas" /> 0} diff --git a/packages/jbrowse-plugin-apollo/test_data/onegene.fasta.gff3 b/packages/jbrowse-plugin-apollo/test_data/onegene.fasta.gff3 new file mode 100644 index 000000000..37572e4f3 --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/onegene.fasta.gff3 @@ -0,0 +1,25 @@ +##gff-version 3 +ctgA example gene 1 100 . + . ID=gx1 +ctgA example mRNA 1 100 . + . ID=tx1;Parent=gx1 +ctgA example exon 1 100 . + . ID=cds1;Parent=tx1 +##FASTA +>ctgA +cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat +tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg +aattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaacc +ctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca +acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctag +atagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatac +gagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtaccc +aggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattc +tgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggt +tgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttacctta +gattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggt +accataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcct +cctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaa +ttaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaat +cgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttac +gacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttatt +gctacacaggctcttgtagacgacctacttagcactacggccgagcgcaataacccccgg +aaagcacttgctactgggaggcgggtttatccatcggcaataggggttatcagtactacc +aagaagattgtgaagatattaacagcattgaaaaaagttcggactgggcatgaaacgtgt diff --git a/packages/jbrowse-plugin-apollo/test_data/space.gff3 b/packages/jbrowse-plugin-apollo/test_data/space.gff3 new file mode 100644 index 000000000..5188e57ee --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/space.gff3 @@ -0,0 +1,905 @@ +##gff-version 3 +ctgA example gene 1050 9000 . + . ID=EDEN +ctgA est EST_match 1150 7200 . + . ID=Match1;Target=agt 1 +ctgA est EST_match 5410 7503 . - . ID=Match2;Target=agt 1 +ctgA est EST_match 7500 8000 . - . ID=Match3;Target=agt A +ctgA est EST_match 8000 9000 . - . ID=Match4;Target=agt B +ctgA est EST_match 9520 9900 . - . ID=Match5;Target=agt_1 +##FASTA +>ctgA +cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat +tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg +aattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaacc +ctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca +acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctag +atagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatac +gagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtaccc +aggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattc +tgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggt +tgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttacctta +gattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggt +accataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcct +cctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaa +ttaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaat +cgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttac 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+tgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagtag +tagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtata +gagattatgtcactccgtcac +>ctgB +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATG diff --git a/packages/jbrowse-plugin-apollo/test_data/volvox.fa b/packages/jbrowse-plugin-apollo/test_data/volvox.fa new file mode 100644 index 000000000..f3bc72334 --- /dev/null +++ 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+ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATG diff --git a/packages/jbrowse-plugin-apollo/test_data/volvox.fasta.gff3 b/packages/jbrowse-plugin-apollo/test_data/volvox.fasta.gff3 new file mode 100644 index 000000000..7e51efcad --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/volvox.fasta.gff3 @@ -0,0 +1,1144 @@ +# Note: See http://song.sourceforge.net +# multi-exon gene - several linked CDSs +# single exon gene - one CDS only +##gff-version 3 +ctgA example contig 1 50001 . . . Name=ctgA;multivalue=val1,val2,val3 +ctgA example BAC 1000 20000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads +ctgA example SNP 1000 1000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1 +ctgA example clone_start 1000 1500 . + . Parent=b101.2 +ctgA example remark 1000 2000 . . . Name=Remark:hga;Alias=hga +ctgA est EST_match 1050 3202 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 654 +ctgA est EST_match 1050 7300 . + . ID=Match3;Name=agt221.5;Target=agt221.5 1 1253 +ctgA est match_part 1050 1500 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451 +ctgA est match_part 1050 1500 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 1 451 +ctgA example gene 1050 9000 . + . ID=EDEN;Name=EDEN;Note=protein kinase +ctgA example mRNA 1050 9000 . + . ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Note=Eden splice form 1;Index=1 +ctgA example mRNA 1050 9000 . + . ID=EDEN.2;Parent=EDEN;Name=EDEN.2;Note=Eden splice form 2;Index=1 +ctgA example five_prime_UTR 1050 1200 . + . Parent=EDEN.1 +ctgA example five_prime_UTR 1050 1200 . + . Parent=EDEN.2 +ctgA example protein_coding_primary_transcript 1100 2000 . + . Name=Gene:hga;Alias=hga +ctgA est EST_match 1150 7200 . + . ID=Match5;Name=agt767.5;Target=agt767.5 1 1153 +ctgA est match_part 1150 1500 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 1 351 +ctgA example polypeptide 1200 1900 . + . Name=Protein:HGA;Alias=hga +ctgA example CDS 1201 1500 . + 0 Parent=EDEN.1 +ctgA example CDS 1201 1500 . + 0 Parent=EDEN.2 +ctgA example mRNA 1300 9000 . + . ID=EDEN.3;Parent=EDEN;Name=EDEN.3;Note=Eden splice form 3;Index=1 +ctgA example five_prime_UTR 1300 1500 . + . Parent=EDEN.3 +ctgA example protein_coding_primary_transcript 1600 3000 . - . Name=Gene:hgb;Alias=hgb +ctgA example remark 1659 1984 . + . Name=f07;Note=This is an example +ctgA example polypeptide 1800 2900 . - . Name=Protein:HGB;Alias=hgb +ctgA est match_part 3000 3202 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654 +ctgA example CDS 3000 3902 . + 0 Parent=EDEN.1 +ctgA example five_prime_UTR 3000 3300 . + . Parent=EDEN.3 +ctgA example remark 3014 6130 . + . Name=f06;Note=This is another example +ctgA example CDS 3301 3902 . + 0 Parent=EDEN.3 +ctgA example remark 4715 5968 . - . Name=f05;Note=Ok! Ok! I get the message. +ctgA est match_part 5000 5500 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 452 952 +ctgA est match_part 5000 5500 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 352 852 +ctgA example CDS 5000 5500 . + 0 Parent=EDEN.1 +ctgA example CDS 5000 5500 . + 0 Parent=EDEN.2 +ctgA example CDS 5000 5500 . + 1 Parent=EDEN.3 +ctgA example match 5233 5302 . - . Name=seg04 +ctgA est EST_match 5410 7503 . - . ID=Match2;Name=agt830.3;Target=agt830.3 1 595 +ctgA est match_part 5410 5500 . - . Parent=Match2;Name=agt830.3;Target=agt830.3 505 595 +ctgA example match 5800 6101 . - . Name=seg04 +ctgA example match 6442 6854 . - . Name=seg04 +ctgA example match 6885 7241 . - . Name=seg03 +ctgA est match_part 7000 7200 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 853 1153 +ctgA est match_part 7000 7300 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 953 1253 +ctgA est match_part 7000 7503 . - . Parent=Match2;Name=agt830.3;Target=agt830.3 1 504 +ctgA example CDS 7000 7600 . + 1 Parent=EDEN.3 +ctgA example CDS 7000 7608 . + 0 Parent=EDEN.1 +ctgA example CDS 7000 7608 . + 0 Parent=EDEN.2 +ctgA example match 7106 7211 . - . Name=seg04 +ctgA example match 7410 7737 . - . Name=seg03 +ctgA est EST_match 7500 8000 . - . ID=Match4;Name=agt221.3;Target=agt221.3 1 501 +ctgA example three_prime_UTR 7601 9000 . + . Parent=EDEN.3 +ctgA example three_prime_UTR 7609 9000 . + . Parent=EDEN.1 +ctgA example three_prime_UTR 7609 9000 . + . Parent=EDEN.2 +ctgA example match 7695 8177 . - . Name=seg04 +ctgA est EST_match 8000 9000 . - . ID=Match6;Name=agt767.3;Target=agt767.3 1 1001 +ctgA example match 8055 8080 . - . Name=seg03 +ctgA example match 8306 8999 . - . Name=seg03 +ctgA example match 8545 8783 . - . Name=seg04 +ctgA example match 8869 8935 . - . Name=seg04 +ctgA example match 9404 9825 . - . Name=seg04 +ctgA bare_predicted CDS 10000 11500 . + 0 Name=Apple1;Note=CDS with no parent +ctgA example polypeptide_domain 11911 15561 . + . Name=m11;Note=kinase +ctgA example match 12531 12895 . + . Name=seg12 +ctgA predicted mRNA 13000 17200 . + 0 ID=cds-Apple2;Name=Apple2;Note=mRNA with CDSs but no UTRs +ctgA example match 13122 13449 . + . Name=seg12 +ctgA example remark 13280 16394 . + . Name=f08 +ctgA example match 13452 13745 . + . Name=seg12 +ctgA predicted CDS 13500 13800 . + 0 Parent=cds-Apple2 +ctgA example polypeptide_domain 13801 14007 . - . Name=m05;Note=helix loop helix +ctgA example match 13908 13965 . + . Name=seg12 +ctgA example match 13998 14488 . + . Name=seg12 +ctgA example match 14564 14899 . + . Name=seg12 +ctgA example polypeptide_domain 14731 17239 . - . Name=m14;Note=kinase +ctgA predicted CDS 15000 15500 . + 1 Parent=cds-Apple2 +ctgA example match 15185 15276 . + . Name=seg12 +ctgA example remark 15329 15533 . + . Name=f10 +ctgA example polypeptide_domain 15396 16159 . + . Name=m03;Note=zinc finger +ctgA example match 15639 15736 . + . Name=seg12 +ctgA example match 15745 15870 . + . Name=seg12 +ctgA predicted CDS 16500 17000 . + 2 Parent=cds-Apple2 +ctgA example polypeptide_domain 17023 17675 . + . Name=m08;Note=7-transmembrane +ctgA exonerate mRNA 17400 23000 . + . ID=rna-Apple3;Name=Apple3;Note=mRNA with both CDSs and UTRs +ctgA exonerate UTR 17400 17999 . + . Parent=rna-Apple3 +ctgA example polypeptide_domain 17667 17690 . + . Name=m13;Note=DEAD box +ctgA exonerate CDS 18000 18800 . + 0 Parent=rna-Apple3 +ctgA example polypeptide_domain 18048 18552 . - . Name=m07;Note=7-transmembrane +ctgA example match 18509 18985 . + . Name=seg08 +ctgA example match 18989 19388 . + . Name=seg08 +ctgA exonerate CDS 19000 19500 . + 1 Parent=rna-Apple3 +ctgA example remark 19157 22915 . - . Name=f13 +ctgA example match 19249 19559 . + . Name=seg06 +ctgA example match 19496 19962 . + . Name=seg08 +ctgA example clone_end 19500 20000 . - . Parent=b101.2 +ctgA example match 19975 20260 . + . Name=seg06 +ctgA example match 20093 20580 . + . Name=seg08 +ctgA example match 20379 20491 . + . Name=seg06 +ctgA example match 20533 21005 . + . Name=seg06 +ctgA example match 20970 21052 . + . Name=seg08 +ctgA exonerate CDS 21000 21200 . + 2 Parent=rna-Apple3 +ctgA example match 21122 21331 . + . Name=seg06 +ctgA exonerate UTR 21201 23000 . + . Parent=rna-Apple3 +ctgA example match 21270 21277 . + . Name=seg08 +ctgA example match 21682 22176 . + . Name=seg06 +ctgA example match 21685 22168 . + . Name=seg08 +ctgA example polypeptide_domain 21748 25612 . + . Name=m12;Note=kinase +ctgA example remark 22132 24633 . + . Name=f15 +ctgA example match 22374 22570 . + . Name=seg06 +ctgA example match 22564 22869 . + . Name=seg08 +ctgA example match 22958 23298 . + . Name=seg08 +ctgA example match 23025 23427 . + . Name=seg06 +ctgA example remark 23072 23185 . + . Name=f14 +ctgA example match 23412 23469 . + . Name=seg08 +ctgA example match 23932 23932 . + . Name=seg08 +ctgA example match 24228 24510 . + . Name=seg11 +ctgA example match 24328 24787 . + . Name=seg08 +ctgA example remark 24562 28338 . + . Name=f02 +ctgA example match 24868 25012 . + . Name=seg11 +ctgA example match 25212 25426 . + . Name=seg11 +ctgA example match 25228 25367 . + . Name=seg08 +ctgA example match 25794 25874 . + . Name=seg11 +ctgA example match 26075 26519 . + . Name=seg11 +ctgA example match 26122 26126 . + . Name=seg02 +ctgA example match 26497 26869 . + . Name=seg02 +ctgA example match 26503 26799 . - . Name=seg05 +ctgA example match 26930 26940 . + . Name=seg11 +ctgA example match 26975 27063 . + . Name=seg11 +ctgA example match 27172 27185 . - . Name=seg05 +ctgA example match 27201 27325 . + . Name=seg02 +ctgA example match 27372 27433 . + . Name=seg02 +ctgA example match 27415 27799 . + . Name=seg11 +ctgA example match 27448 27860 . - . Name=seg05 +ctgA example match 27565 27565 . + . Name=seg02 +ctgA example match 27813 28091 . + . Name=seg02 +ctgA example match 27880 27943 . + . Name=seg11 +ctgA example match 27887 28076 . - . Name=seg05 +ctgA example match 28093 28201 . + . Name=seg02 +ctgA example match 28225 28316 . - . Name=seg05 +ctgA example match 28225 28346 . + . Name=seg11 +ctgA example match 28329 28377 . + . Name=seg02 +ctgA example polypeptide_domain 28332 30033 . - . Name=m02;Note=HOX +ctgA example polypeptide_domain 28342 28447 . - . Name=m10;Note=DEAD box +ctgA example match 28375 28570 . + . Name=seg11 +ctgA example match 28758 29041 . + . Name=seg11 +ctgA example match 28777 29058 . - . Name=seg05 +ctgA example match 28829 29194 . + . Name=seg02 +ctgA example match 29101 29302 . + . Name=seg11 +ctgA example match 29513 29647 . - . Name=seg05 +ctgA example match 29517 29702 . + . Name=seg02 +ctgA example match 29604 29702 . + . Name=seg11 +ctgA example match 29713 30061 . + . Name=seg02 +ctgA example match 29771 29942 . + . Name=seg10 +ctgA example match 29867 29885 . + . Name=seg11 +ctgA example match 30042 30340 . + . Name=seg10 +ctgA example match 30108 30216 . - . Name=seg05 +ctgA example match 30241 30246 . + . Name=seg11 +ctgA example match 30329 30774 . + . Name=seg02 +ctgA example match 30465 30798 . - . Name=seg05 +ctgA example match 30575 30738 . + . Name=seg11 +ctgA example polypeptide_domain 30578 31748 . + . Name=m06;Note=SUSHI repeat +ctgA example match 30808 31306 . + . Name=seg02 +ctgA example match 30810 31307 . + . Name=seg10 +ctgA example match 31232 31236 . - . Name=seg05 +ctgA example match 31421 31817 . - . Name=seg05 +ctgA example match 31516 31729 . + . Name=seg02 +ctgA example match 31753 32154 . + . Name=seg02 +ctgA example match 31761 31984 . + . Name=seg10 +ctgA example match 32010 32057 . - . Name=seg05 +ctgA example match 32208 32680 . - . Name=seg05 +ctgA example match 32329 32359 . + . Name=seg01 +ctgA example match 32374 32937 . + . Name=seg10 +ctgA example match 32595 32696 . + . Name=seg02 +ctgA example match 32892 32901 . + . Name=seg02 +ctgA example match 33053 33325 . - . Name=seg05 +ctgA example match 33127 33388 . + . Name=seg02 +ctgA example polypeptide_domain 33325 35791 . + . Name=m04;Note=Ig-like +ctgA example match 33438 33868 . - . Name=seg05 +ctgA example match 33439 33443 . + . Name=seg02 +ctgA example match 33759 34209 . + . Name=seg02 +ctgA example match 34244 34313 . - . Name=seg05 +ctgA example match 34401 34466 . + . Name=seg02 +ctgA example match 34605 34983 . - . Name=seg05 +ctgA example match 35333 35507 . - . Name=seg05 +ctgA example match 35642 35904 . - . Name=seg05 +ctgA example remark 36034 38167 . + . Name=f09 +ctgA example match 36616 37057 . - . Name=seg09 +ctgA example remark 36649 40440 . - . Name=f03 +ctgA example match 37208 37227 . - . Name=seg09 +ctgA example remark 37242 38653 . + . Name=f04 +ctgA example polypeptide_domain 37497 40559 . - . Name=m15;Note=7-transmembrane +ctgA example match 39265 39361 . - . Name=seg15 +ctgA example match 39753 40034 . - . Name=seg15 +ctgA example match 40515 40954 . - . Name=seg15 +ctgA example match 41137 41318 . - . Name=seg14 +ctgA example match 41252 41365 . - . Name=seg15 +ctgA example match 41492 41504 . - . Name=seg15 +ctgA example match 41754 41948 . - . Name=seg14 +ctgA example match 41941 42377 . - . Name=seg15 +ctgA example match 42057 42474 . - . Name=seg14 +ctgA example match 42748 42954 . - . Name=seg15 +ctgA example match 42890 43270 . - . Name=seg14 +ctgA example match 43395 43811 . - . Name=seg14 +ctgA example match 43401 43897 . - . Name=seg15 +ctgA example match 44043 44113 . - . Name=seg15 +ctgA example match 44065 44556 . - . Name=seg14 +ctgA example match 44191 44514 . - . Name=seg07 +ctgA example match 44399 44888 . - . Name=seg15 +ctgA example match 44552 45043 . - . Name=seg07 +ctgA example remark 44705 47713 . - . Name=f01 +ctgA example match 44763 45030 . - . Name=seg14 +ctgA example match 45231 45488 . - . Name=seg14 +ctgA example match 45281 45375 . - . Name=seg15 +ctgA example match 45373 45600 . - . Name=seg07 +ctgA example match 45711 46041 . - . Name=seg15 +ctgA example match 45790 46022 . - . Name=seg14 +ctgA example match 45897 46315 . - . Name=seg07 +ctgA example polypeptide_domain 46012 48851 . + . Name=m09;Note=kinase +ctgA example match 46092 46318 . - . Name=seg14 +ctgA example match 46425 46564 . - . Name=seg15 +ctgA example match 46491 46890 . - . Name=seg07 +ctgA example match 46738 47087 . - . Name=seg15 +ctgA example match 46816 46992 . - . Name=seg14 +ctgA example remark 46990 48410 . - . Name=f11 +ctgA example match 47126 47297 . - . Name=seg07 +ctgA example match 47329 47595 . - . Name=seg15 +ctgA example match 47449 47829 . - . Name=seg14 +ctgA example match 47735 47983 . - . Name=seg07 +ctgA example match 47858 47979 . - . Name=seg15 +ctgA example match 48169 48453 . - . Name=seg15 +ctgA example polypeptide_domain 48253 48366 . + . Name=m01;Note=WD40 +ctgA example match 48447 48709 . - . Name=seg07 +ctgA example match 48931 49186 . - . Name=seg07 +ctgA example match 49406 49476 . + . Name=seg13 +ctgA example match 49472 49699 . - . Name=seg07 +ctgA example remark 49758 50000 . - . Name=f12 +ctgA example match 49762 50000 . + . Name=seg13 +ctgA example match 49957 50000 . - . Name=seg07 +ctgA example match 49957 50000 . - . Name=seg07 +ctgB example contig 1 6079 . . . Name=ctgB +ctgB example remark 1659 1984 . + . Name=f07;Note=This is an example +ctgB example remark 3014 6130 . + . Name=f06;Note=This is another example +ctgB example remark 4715 5968 . - . Name=f05;Note=ああ、この機能は、世界中を旅しています！ +##FASTA +>ctgA +cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat +tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg +aattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaacc +ctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca +acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctag +atagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatac +gagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtaccc +aggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattc +tgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggt +tgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttacctta +gattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggt +accataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcct +cctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaa +ttaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaat +cgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttac 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+atagtgtgtcgagtcgttatacaatacatactccaagcgtactccctttgggtaacgggt +ttgggtacatattaccatggtgtggaccgatttgtaaccctataagcgttccgggtactt +taccatcgcggatgcgatcgcggatctacctatgtcagcgacatactgcccgtccaaaag +tgattcagtatgtgttaatcagcgtattgcatcatcagtcattgagagtggaccgttctc +gaagagcaagattcctgaccctttccactgggccatccagtacacccaattatatgcaga +cgaaaagctccatacatatataatacctcttcacaccgtgtgcagagaccaacttgatcg +atattgtactcactcgtacggaataattagaagggcccgactgtcgagaccgttagcatt +tgcattatcgcggtgagcgtatagaaacaattataggctttgctgcgatcgcagtgtctg +ggacagagtctcctagacctagatcagcttaaaacaatgattgtaggtaatgtgcgttgc +cgtcgggccacacctttcagttcggttacaccgactcagaattatcttctatcgggaccc +tcaaactgataatggggtcaaatggtggtggtcccgtctttctgcagtgctttgtgagca +gaatagctctcgagcgctccagtacgcctgagtatggctgcgcccaccaattggcgccgt +taatgcgtggcgacacaagagaaccagtccacataagttatgcccttaagaagatcaccg +ggtttgcgccatcctgattcaggtaacggacgtccgtgtacacgaaccatactaatgagt +tctacatcgctccaacgcgtcttgaaccctatcgacaattacaaatgcaaagtattagtt +gggtcagtgcgtagcttatccaagggctgcagtaagtcgtccccatgacagacggacggc +ataagggccaaaaattccgccgcattagctgttaataatgccatccagaaccggacagtc +tcgatatataacttacggctgcgaactggcccttatgaattacatccacgtgctagttaa +caggacggatcgcccggactaattgccgatcggccgtcccattctccgtacgatgtactg +aacccaggcgtgtgaatgggtatgtcaacgtttacccatcgaccctgcctatagacctga +gtttcattccagttgagcgtagaatgggatgagcagctttgcttgaggtgcgatattcgg +gagacctggtcagcaggattgatggttttatagtgctggattccctgctgaaattctctc +ttctgccgcatgtgaagaaggccttgcttcccttccacatgattgtaagatttcctaagg +cctcccagctgcgtggaactgtgagtcaattaaacctctttcctttataaattacccagt +ctcaggtatttccttatcgtggtatgagaacggattaatacagttgtgtaagccagctcc +ttataataaatctctctccctctctctgcctctcatctatgtatgtatgtatctgtcatc +tatctcctataagttgtttcttttgagaactctgactaacatagacattaaataaacaat +ttgtatactgaataattatataactactgcttgggggtgtggttgtgttgtgtggtgagg +gggtgtagaaatgtctaggggttgatctagcctaacaccttccagatgaccctaggttct +ggcctttccccaaagagtcctggtctactcagtcatctcccacaatttggccatcttctt +gggtgctcaggacaataaatgacccagccagatcctctagagtcgacctgcaggcatgca +agcttggcgtaatcatggtcatagctgtttgctgtgtgaaattgttatgcgctcacattg +cacacaacatacgagccggaagcatacagtgtagagcctggggtggcgtatgagtgagct +aactcacattaatttgcgtttgcgctcactgccgcttttcagtcggggaaactgtcgtga +cagctgcatttaatgatcggtcatcgcgcggggagatgcggttttgcgtattgtgccgca +ggtggttatttctctcaacagtgagacgggcacagctgattgccctcaccggctgggctg +agagagttgcagcaagcgtacacgcggggtttgcccagcagggcgaaattcctgttgtga +tgtggattccgaatcgggcaaatgccctataaatcaaagcatagtccgagatagggtttg +agtgtgttcagttttgggacagaggtcactataaagaacgttgactgcacgtcaagggcg +agaaacgtcatcaggcgattgcactacgtgacatcaccaatcagttttttgggtcaggtg +cgtgagacttatcggaactaaaggagcccgttttagcttcggggaaacgcgaagtgtcgg +aagaaggaaaacgaagagcgggtatcgcggaatgtacgtgctgagcgaaaccaacgcgcg +ttacggtcaagcgtgtatgtgttttggaggtaagtttccctgataaagcggaacaggggc +tatgtgtttacgggggtcgcatggagtacaagggggcaggacaagatttgcgcgacatgg +ttttttttaaattgcgggagatggttggctgtcccgatgagattagaacctgcttttgtt +ttagtttcggttcggtcagttcggactttggattggttttgttgggtatttaagaagggt +gtttgtgggatgtttttttttgggtcgagcatcactggactatgtgtgtcctgcgtatcg +tggcggggcctcgaacttagaggtaggacgattccgatgcaacaaccttatgctttactc +caagcgatggtgaggcaaccttgtacagaagtgcaaccgccattgtggctgggtcggccc +aaggaacggatattctcctgggtactgacaacccaggtctactgggttctatcgacggta +cagtcaagcctcgagtttactgtctcccacttaagtccgctctgggcattaatgagtctg +tggggtatcaagggtcacccaacgaagtagctagtcccgttgtacatttcgcgcgttacc +tagggagcacggtgagctacgagggtgtagctgcacacagcacggtatataggaacgcaa +acatagtagtatgtccctatgcataacagggagaagtgactctccgacggtcatttatcc +cagactctcctcgctccctactaattgttctatatacaatcggagtaaattggtacctct +ctgacaacataggggggttgaagtttatgccacgcagtctgttacacttttgccggggaa +ttgtgtagaccatgactcaaggtggtggtgcgagttactctactatctactgcttctcat +tacacatctcttggcttacaggccccagttatcagttacgaggctgccttaagagaaggc +caacattcatgatcagatccccgcacacgggatgatagtctgagatctgccggacgctcg +tctgctacaagtgtgggttgagcatagggtaagcctaagggctcgtaatggtacttcgcg +atgtttattcgatatgagctacaaggtataacgttgccttcaccatttcggctcacgact +cttacctcgcctcaccgctagacaccctgaccaaccgttagggtactgacaaccgatcag +gcgactcctaaaggacctctcagcctcccagacatgaggtccgctcgcatgctgttcagc +gagtccatatcaggaacagcaacgagacaaggcgagagcaacactagacttggagacata +ccaccacatctgtttactcttgattcaggaagacctgtggtaactgggcgacgcgtgcgt +ttatccgtcttccaatctccacagaatctgctccgtcagagggatgtatgactaacgcac +tgattttttgttcagtaaccgggcgcggattacggggcgtattccaggggtacattcaac +gggaccccaaggaaaagttcggggtatttaaggaggcggtccaactctcggacttattgg +gcgacgtaatgataagcacacctctgctcatacagtgcacgaagaccggcattgttcaaa +cacagccgtccattccgcgactattgtcctgtgtacaggtgcctcgggtcccaaatccag +cttatacccaaaactctcccggacttttttcgtccttgcaggaggaaaggacctgactcc +acgtttattaggggatcgttgggcccggacaatcgtgtattcaacataataaatgggttc +tagtttaaagccggaggtgacggtggattatggactagaggtaaacatttccggcgtagg +tcagaaagaatatagaccctaaatttacgcaaaacgtgcacacgattgtaggtggagtcg +tattaggaactcagggcgggtggaacgagtgtgttttaggcttaccatgaaccgtcgcgc +ggaaaatgatgacagaatggacggtgcttttttgcggggccaacaaaactcgcttatgtt +cgccattggatgtaagtaccgctatactacgcagcgaccccttacgacattgttgatttc +caatgctttcatggaggtttgtgagcggtcgctaggaatcttcctccagcgagtagccag +ctggccactagttagcaaccagagttcatatgagctccagtaacacgaaggtacataagg +aacgcaagcaagttcgggactacatagaacttggggtgcgtctaagccggggatcttaat +agacaagaggccatcgtatgggtcaaatttcatgtttcgtcagatgccctatccgtggac +acctaaatcaagcatcatatcctaatgctatttgctctcgctttggtatgattcatatgc +agccctgtccgtaaaatgacgggccagaggatacctgtcactacctatttcagattacca +ctgttcgaaaccttgctctgaaatcgatcttcgtagagtgttcgttaatcgccgcgtgaa +ttatataatcccccaaggagtacccttcgtcggtgcagtctacgtaactttcccaggtta +gcccccatctaatcgacgtacgtgagggggctacgggagatcgcacaagccgaagcattt +ctgctctgtttcgttacaactggaatcctcatcacgcagcgctaccggatgccatcccta +gtcatccccgcgagtttaaccagtcgagatggctcgaaccgtgtttcgaaggctggctat +tgaaccagttataaagcaggggcgactgtccgtcggacttcgatataaactatcacaaat +ttggcataagtatatacagccaagaaggctcagataggcacacgcacccaaatagtgacc +gcctacgttcaggttgcccggcaacgaagcgcgcttgctccattaatccactatcagagg +taacgaccctctttcaccgtagctgcccccatgtcggggcaacagtttcccaccgataac +gtgttctgtctagtacgtgaaacggattggctaacccctgtcagcctaattagatgacat +cctcgtacctctagagaaggtgaggagaccgctggaacataagtaaacagtttaccaaac +aatgatcatacatataacagaaaggagagatgcccggtggggtcgaagatacagctgtgg +ttgatatctgcaacggccaggctgtcatgaagatcacgcgcacgaagctatttatgaaag +atacccatgccggggcggcagcggtacctagtcctaaataccgacacgtagcaacgcgtc +ccctgaggcccaccctagtcaagggaacttaaaatatacgctgactttgtctaccaatca +tcttcgattaacaccggcatactaagtctaccctggacccagcaatgagaaaaacttttc +cgaatgatcattgtgagtttacagagattaggaacaccaaaaaaatttacgtacgtccgg +ttacccctgtgtgacccttggccacaaaccgtaaggtgcagcatgggcgttgagtccagg +gtttgtgacaccagacatgaataccctgtggcgggttgttagcatgttattcggatccga +tttcagagggtccgttgataccgggcagtacaagacaccccacaccactgaggtggtacg +tccgccagtctgctccctacgttatgcaaaattccttccccggcgttcttgcctgtacta +ctcctaaagggccgtgaaatccgacgttgctgctccgtctcgggacacccacacaacagc +tacggaaaatcgtgaggatgcacaagggtcttgcattgttgatctatacagctcttcgca +cggtgtgctactgttttccacaatgggcaaggggcgtgtaggtcttatgtaggagtaccc +cgtgatctggctataccttgctatctattccaccaaaatagccggggtcttatagtttta +ttccggatctatcaagtgacaagtccatggggtaaacggtaagtttcgtacgctgggcgg +tgatccccgcttataaacgagcaaaccgccaaagcaaccattgccgggcttccagctagt +aaatgttgggtgtcaatcgtgcatgtgactacttacccacaaagggacgcttgaagcgcc +tgaactcgtcacgtcatgcctagctcccggttgaaacacgaagacgcgtgaacctatctt +tgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagtag +tagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtata +gagattatgtcactccgtcac +>ctgB +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATG diff --git a/packages/jbrowse-plugin-apollo/test_data/volvox2.fasta.gff3 b/packages/jbrowse-plugin-apollo/test_data/volvox2.fasta.gff3 new file mode 100644 index 000000000..dd20354fb --- /dev/null +++ b/packages/jbrowse-plugin-apollo/test_data/volvox2.fasta.gff3 @@ -0,0 +1,906 @@ +# Note: See http://song.sourceforge.net +# multi-exon gene - several linked CDSs +# single exon gene - one CDS only +##gff-version 3 +ctgA example BAC 1000 20000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads +ctgA example SNP 1000 1000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1 +ctgA example clone_start 1000 1500 . + . Parent=b101.2 +ctgA example remark 100 200 . . . Name=SpamGene; +##FASTA +>ctgA +cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat +tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg +aattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaacc +ctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca +acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctag +atagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatac +gagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtaccc +aggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattc +tgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggt +tgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttacctta +gattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggt +accataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcct +cctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaa +ttaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaat +cgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttac 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+atacccatgccggggcggcagcggtacctagtcctaaataccgacacgtagcaacgcgtc +ccctgaggcccaccctagtcaagggaacttaaaatatacgctgactttgtctaccaatca +tcttcgattaacaccggcatactaagtctaccctggacccagcaatgagaaaaacttttc +cgaatgatcattgtgagtttacagagattaggaacaccaaaaaaatttacgtacgtccgg +ttacccctgtgtgacccttggccacaaaccgtaaggtgcagcatgggcgttgagtccagg +gtttgtgacaccagacatgaataccctgtggcgggttgttagcatgttattcggatccga +tttcagagggtccgttgataccgggcagtacaagacaccccacaccactgaggtggtacg +tccgccagtctgctccctacgttatgcaaaattccttccccggcgttcttgcctgtacta +ctcctaaagggccgtgaaatccgacgttgctgctccgtctcgggacacccacacaacagc +tacggaaaatcgtgaggatgcacaagggtcttgcattgttgatctatacagctcttcgca +cggtgtgctactgttttccacaatgggcaaggggcgtgtaggtcttatgtaggagtaccc +cgtgatctggctataccttgctatctattccaccaaaatagccggggtcttatagtttta +ttccggatctatcaagtgacaagtccatggggtaaacggtaagtttcgtacgctgggcgg +tgatccccgcttataaacgagcaaaccgccaaagcaaccattgccgggcttccagctagt +aaatgttgggtgtcaatcgtgcatgtgactacttacccacaaagggacgcttgaagcgcc +tgaactcgtcacgtcatgcctagctcccggttgaaacacgaagacgcgtgaacctatctt 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+ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGAT +ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGCCTGATGCTGATACATGCTAGCTACGTGCATGCTCGACATG diff --git a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json b/packages/jbrowse-plugin-apollo/tsconfig.eslint.json index 0cc67dc02..673840016 100644 --- a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json +++ b/packages/jbrowse-plugin-apollo/tsconfig.eslint.json @@ -5,5 +5,5 @@ "noEmit": true, "allowJs": true }, - "include": ["cypress.config.js", "jest.config.js", "jestSetup.js", "rollup.config.js"], + "include": ["jest.config.js", "jestSetup.js", "rollup.config.js"], } diff --git a/yarn.lock b/yarn.lock index f8a60af77..03e5fd757 100644 --- a/yarn.lock +++ b/yarn.lock @@ -4084,6 +4084,15 @@ __metadata: languageName: node linkType: hard +"@mongodb-js/saslprep@npm:^1.1.0": + version: 1.1.0 + resolution: "@mongodb-js/saslprep@npm:1.1.0" + dependencies: + sparse-bitfield: ^3.0.3 + checksum: 1479a43e216734672f8eb1a2a55165b6896841bd00fb5bd645390a24374ef6c29f0f6d19a43618a19b8f1912fcbd2b2cc2210a62361103d1f28dce6852cf31d4 + languageName: node + linkType: hard + "@mui/base@npm:5.0.0-alpha.119, @mui/base@npm:^5.0.0-alpha.118": version: 5.0.0-alpha.119 resolution: "@mui/base@npm:5.0.0-alpha.119" @@ -7886,16 +7895,7 @@ __metadata: languageName: node linkType: hard -"bson@npm:^4.6.2, bson@npm:^4.6.3": - version: 4.6.5 - resolution: "bson@npm:4.6.5" - dependencies: - buffer: ^5.6.0 - checksum: b9d4856241e76f6bacf6825b5280f993a867b74fa47bb62b3a20d835d9f02979e1a10a6c38536ac86cb485dc96aabdacb0c6922fca7a784603a781a00e23c336 - languageName: node - linkType: hard - -"bson@npm:^4.7.0, bson@npm:^4.7.2": +"bson@npm:^4, bson@npm:^4.6.2, bson@npm:^4.6.3, bson@npm:^4.7.0, bson@npm:^4.7.2": version: 4.7.2 resolution: "bson@npm:4.7.2" dependencies: @@ -7905,9 +7905,16 @@ __metadata: linkType: hard "bson@npm:^5.0.1": - version: 5.0.1 - resolution: "bson@npm:5.0.1" - checksum: c8b028cdad57ab967d8deb4895d1341d84cd350c20137e9949ebd7924e408e81921fa5fcd17e07bc3aa3bca99a49208e95f0ab9606686b980af2eaf798b56e1f + version: 5.4.0 + resolution: "bson@npm:5.4.0" + checksum: 1c07e3d09f139d414bd226bf7f4e9aaa7a726e0c9718c55b53bb23ffa2805cac8b66e4fa46b424c73a35c6e292ed5f7432df5c76ea5d08052642b2ac9e0399e3 + languageName: node + linkType: hard + +"bson@npm:^6.0.0": + version: 6.0.0 + resolution: "bson@npm:6.0.0" + checksum: 594ebbfcaef8487741405915977b5d38dcd6e36b08af54faf459a8e8d039d555a2db2bb422c8d25b065ac9b5bb9828bc8cc49aa145194f53f8352d355fd83a77 languageName: node linkType: hard @@ -9011,6 +9018,15 @@ __metadata: languageName: node linkType: hard +"cypress-mongodb@npm:^6.2.0": + version: 6.2.0 + resolution: "cypress-mongodb@npm:6.2.0" + dependencies: + mongodb: 6.0.0 + checksum: 15dce27eaf22c70fb530a2d8637a07af17f978b93baba492bc6ef68d98f63808d5aab8556fee8b82e97c8c94942ddcc10330d6e8e09fe2c9f6fb9a7ff049d974 + languageName: node + linkType: hard + "cypress@npm:*": version: 10.3.1 resolution: "cypress@npm:10.3.1" @@ -12910,6 +12926,7 @@ __metadata: bson-objectid: ^2.0.3 clsx: ^1.1.1 cypress: ^12.17.2 + cypress-mongodb: ^6.2.0 fake-indexeddb: ^4.0.2 fast-deep-equal: ^3.1.3 file-saver: ^2.0.5 @@ -15872,6 +15889,40 @@ __metadata: languageName: node linkType: hard +"mongodb@npm:6.0.0": + version: 6.0.0 + resolution: "mongodb@npm:6.0.0" + dependencies: + "@mongodb-js/saslprep": ^1.1.0 + bson: ^6.0.0 + mongodb-connection-string-url: ^2.6.0 + peerDependencies: + "@aws-sdk/credential-providers": ^3.188.0 + "@mongodb-js/zstd": ^1.1.0 + gcp-metadata: ^5.2.0 + kerberos: ^2.0.1 + mongodb-client-encryption: ">=6.0.0 <7" + snappy: ^7.2.2 + socks: ^2.7.1 + peerDependenciesMeta: + "@aws-sdk/credential-providers": + optional: true + "@mongodb-js/zstd": + optional: true + gcp-metadata: + optional: true + kerberos: + optional: true + mongodb-client-encryption: + optional: true + snappy: + optional: true + socks: + optional: true + checksum: 0399d1297795eb8b7bc20c2038085a6928fbd43931d831cd4ef00d8d63a55c8e867d5dfa36859fe69a86ae84fd36d9e5fb9eec1411d351cf653a82894c4751d0 + languageName: node + linkType: hard + "mongodb@npm:^4.7.0": version: 4.16.0 resolution: "mongodb@npm:4.16.0"