@jbrowse/plugin-sequence 2.5.0 → 2.6.2

package/esm/ReferenceSequenceTrack/configSchema.js.map

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package/esm/ReferenceSequenceTrack/index.js.map

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package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map

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package/esm/SequenceSearchAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/SequenceSearchAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/TwoBitAdapter/TwoBitAdapter.js.map

@@ -1 +0,0 @@
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package/esm/TwoBitAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/TwoBitAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/createExtensionPoints.js.map

@@ -1 +0,0 @@
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package/esm/index.js.map

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package/src/BgzipFastaAdapter/BgzipFastaAdapter.test.ts

@@ -1,40 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import Adapter from './BgzipFastaAdapter'
-import configSchema from './configSchema'
-
-test('can use a indexed fasta with gzi', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      fastaLocation: {
-        localPath: require.resolve('../../test_data/volvox.fa.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      faiLocation: {
-        localPath: require.resolve('../../test_data/volvox.fa.gz.fai'),
-        locationType: 'LocalPathLocation',
-      },
-      gziLocation: {
-        localPath: require.resolve('../../test_data/volvox.fa.gz.gzi'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray).toMatchSnapshot()
-
-  const features2 = adapter.getFeatures({
-    refName: 'ctgC',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray2 = await features2.pipe(toArray()).toPromise()
-  expect(featuresArray2).toMatchSnapshot()
-})

package/src/BgzipFastaAdapter/BgzipFastaAdapter.ts

@@ -1,19 +0,0 @@
-import { BgzipIndexedFasta } from '@gmod/indexedfasta'
-import { FileLocation } from '@jbrowse/core/util/types'
-import { openLocation } from '@jbrowse/core/util/io'
-import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter'
-
-export default class extends IndexedFasta {
-  public async setupPre() {
-    const fastaLocation = this.getConf('fastaLocation')
-    const faiLocation = this.getConf('faiLocation')
-    const gziLocation = this.getConf('gziLocation')
-    const fastaOpts = {
-      fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
-      fai: openLocation(faiLocation as FileLocation, this.pluginManager),
-      gzi: openLocation(gziLocation as FileLocation, this.pluginManager),
-    }
-
-    return { fasta: new BgzipIndexedFasta(fastaOpts) }
-  }
-}

package/src/BgzipFastaAdapter/__snapshots__/BgzipFastaAdapter.test.ts.snap

@@ -1,15 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`can use a indexed fasta with gzi 1`] = `
-[
-  {
-    "end": 20000,
-    "refName": "ctgA",
-    "seq": 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c",
-    "start": 0,
-    "uniqueId": "ctgA 0-20000",
-  },
-]
-`;
-
-exports[`can use a indexed fasta with gzi 2`] = `[]`;

package/src/BgzipFastaAdapter/configSchema.ts

@@ -1,51 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-/**
- * #config BgzipFastaAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const BgzipFastaAdapter = ConfigurationSchema(
-  'BgzipFastaAdapter',
-  {
-    /**
-     * #slot
-     */
-    fastaLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
-    },
-    /**
-     * #slot
-     */
-    faiLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/seq.fa.gz.fai',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    metadataLocation: {
-      description: 'Optional metadata file',
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/fa.metadata.yaml',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     */
-    gziLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/seq.fa.gz.gzi',
-        locationType: 'UriLocation',
-      },
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default BgzipFastaAdapter

package/src/BgzipFastaAdapter/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'BgzipFastaAdapter',
-        displayName: 'Bgzip-indexed FASTA adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () =>
-          import('./BgzipFastaAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/ChromSizesAdapter/ChromSizesAdapter.test.ts

@@ -1,27 +0,0 @@
-import Adapter from './ChromSizesAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch sequence from volvox.chrom.sizes', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      chromSizesLocation: {
-        localPath: require.resolve('./test_data/volvox.chrom.sizes'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const regions = await adapter.getRegions()
-  expect(regions).toEqual([
-    {
-      refName: 'ctgA',
-      start: 0,
-      end: 50001,
-    },
-    {
-      refName: 'ctgB',
-      start: 0,
-      end: 6079,
-    },
-  ])
-})

package/src/ChromSizesAdapter/ChromSizesAdapter.ts

@@ -1,51 +0,0 @@
-import {
-  RegionsAdapter,
-  BaseAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-
-export default class extends BaseAdapter implements RegionsAdapter {
-  // the map of refSeq to length
-  protected setupP?: Promise<{ [key: string]: number }>
-
-  async setupPre() {
-    const pm = this.pluginManager
-    const file = openLocation(this.getConf('chromSizesLocation'), pm)
-    const data = await file.readFile('utf8')
-    return Object.fromEntries(
-      data
-        .split(/\n|\r\n|\r/)
-        .map(f => f.trim())
-        .filter(f => !!f)
-        .map((line: string) => {
-          const [name, length] = line.split('\t')
-          return [name, +length]
-        }),
-    )
-  }
-
-  async setup() {
-    if (!this.setupP) {
-      this.setupP = this.setupPre().catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  public async getRegions() {
-    const refSeqs = await this.setup()
-    return Object.keys(refSeqs).map(refName => ({
-      refName,
-      start: 0,
-      end: refSeqs[refName],
-    }))
-  }
-
-  public getHeader() {
-    return {}
-  }
-
-  public freeResources(/* { region } */): void {}
-}

package/src/ChromSizesAdapter/configSchema.ts

@@ -1,25 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config ChromSizesAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const ChromSizesAdapter = ConfigurationSchema(
-  'ChromSizesAdapter',
-  {
-    /**
-     * #slot
-     */
-    chromSizesLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/species.chrom.sizes',
-        locationType: 'UriLocation',
-      },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default ChromSizesAdapter

package/src/ChromSizesAdapter/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'ChromSizesAdapter',
-        displayName: 'Chrom sizes adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () =>
-          import('./ChromSizesAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/ChromSizesAdapter/test_data/volvox.chrom.sizes

@@ -1,2 +0,0 @@
-ctgA	50001
-ctgB	6079

package/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx

@@ -1,161 +0,0 @@
-import React from 'react'
-import { render } from '@testing-library/react'
-import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import DivSequenceRendering from './DivSequenceRendering'
-import DivRenderingConfigSchema from '../configSchema'
-
-// This just keeps our testing logs clean by not displaying `console.error`s
-// from errors we intentionally throw in our tests. Hopefully React will
-// someday provide a way for error boundaries to prevent error logging so we
-// won't have to do this: https://github.com/facebook/react/issues/15069
-const originalError = console.error
-beforeAll(() => {
-  console.error = (...args) => {
-    if (
-      args[0].includes('feature one did not contain a valid `seq` attribute') ||
-      args[0].includes(
-        'The above error occurred in the <SequenceDivs> component',
-      )
-    ) {
-      return
-    }
-    originalError.call(console, ...args)
-  }
-})
-
-afterAll(() => {
-  console.error = originalError
-})
-
-test('renders with one, zoomed way out', () => {
-  const { container } = render(
-    <DivSequenceRendering
-      regions={[
-        { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
-      ]}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({
-              uniqueId: 'one',
-              start: 1,
-              end: 3,
-              seq: 'AB',
-            }),
-          ],
-        ])
-      }
-      config={DivRenderingConfigSchema.create({})}
-      bpPerPx={3}
-    />,
-  )
-
-  expect(container).toMatchSnapshot()
-})
-
-test('renders with one feature with no seq, zoomed in, should throw', () => {
-  const { container } = render(
-    <DivSequenceRendering
-      regions={[
-        { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
-      ]}
-      features={
-        new Map([
-          ['one', new SimpleFeature({ uniqueId: 'one', start: 1, end: 3 })],
-        ])
-      }
-      config={DivRenderingConfigSchema.create({})}
-      bpPerPx={0.05}
-    />,
-  )
-
-  expect(container).toMatchSnapshot()
-})
-
-test('renders with one feature with an incorrect seq, zoomed in, should throw', () => {
-  const { container } = render(
-    <DivSequenceRendering
-      regions={[
-        { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
-      ]}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({
-              uniqueId: 'one',
-              start: 1,
-              end: 3,
-              seq: 'ABC',
-            }),
-          ],
-        ])
-      }
-      config={DivRenderingConfigSchema.create({})}
-      bpPerPx={0.05}
-    />,
-  )
-
-  expect(container).toMatchSnapshot()
-})
-
-test('renders with one feature with a correct seq, zoomed in, should render nicely', () => {
-  const { container } = render(
-    <DivSequenceRendering
-      regions={[
-        { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 },
-      ]}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({
-              uniqueId: 'one',
-              start: 1,
-              end: 10,
-              seq: 'ABCDEFGHI',
-            }),
-          ],
-        ])
-      }
-      config={DivRenderingConfigSchema.create({})}
-      bpPerPx={0.05}
-    />,
-  )
-
-  expect(container).toMatchSnapshot()
-})
-
-test('renders with one feature reversed with a correct seq, zoomed in, should render nicely', () => {
-  const { container } = render(
-    <DivSequenceRendering
-      regions={[
-        {
-          assemblyName: 'volvox',
-          refName: 'zonk',
-          start: 0,
-          end: 1000,
-          reversed: true,
-        },
-      ]}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({
-              uniqueId: 'one',
-              start: 1,
-              end: 10,
-              seq: 'ABCDEFGHI',
-            }),
-          ],
-        ])
-      }
-      config={DivRenderingConfigSchema.create({})}
-      bpPerPx={0.05}
-    />,
-  )
-
-  expect(container).toMatchSnapshot()
-})