@jbrowse/plugin-variants 2.5.0 → 2.6.2

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

@@ -1,325 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch variants from volvox.vcf.gz 1`] = `
-[
-  "ctgA",
-]
-`;
-
-exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
-[
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        3,
-      ],
-      "DP4": [
-        0,
-        0,
-        3,
-        0,
-      ],
-      "FQ": [
-        -36,
-      ],
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0186,
-      ],
-    },
-    "POS": 277,
-    "QUAL": 10.4,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 277,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          13,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          42,
-          9,
-          0,
-        ],
-      },
-    },
-    "start": 276,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604453",
-  },
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        23,
-      ],
-      "DP4": [
-        0,
-        1,
-        8,
-        14,
-      ],
-      "FQ": [
-        -73,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        1,
-        1,
-        0.42,
-        1,
-      ],
-      "VDB": [
-        0.0308,
-      ],
-    },
-    "POS": 1694,
-    "QUAL": 107,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 1694,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          89,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          140,
-          46,
-          0,
-        ],
-      },
-    },
-    "start": 1693,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604551",
-  },
-  {
-    "ALT": [
-      "G",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        1,
-      ],
-      "AF1": [
-        0.5,
-      ],
-      "DP": [
-        22,
-      ],
-      "DP4": [
-        6,
-        5,
-        3,
-        8,
-      ],
-      "FQ": [
-        45.3,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        0.39,
-        1,
-        1,
-        1,
-      ],
-      "VDB": [
-        0.0253,
-      ],
-    },
-    "POS": 2644,
-    "QUAL": 44,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> G",
-    "end": 2644,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          75,
-        ],
-        "GT": [
-          "0/1",
-        ],
-        "PL": [
-          74,
-          0,
-          77,
-        ],
-      },
-    },
-    "start": 2643,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604668",
-  },
-  {
-    "ALT": [
-      "A",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        19,
-      ],
-      "DP4": [
-        0,
-        0,
-        8,
-        11,
-      ],
-      "FQ": [
-        -84,
-      ],
-      "MQ": [
-        36,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3213,
-    "QUAL": 124,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> A",
-    "end": 3213,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          99,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          157,
-          57,
-          0,
-        ],
-      },
-    },
-    "start": 3212,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604785",
-  },
-  {
-    "ALT": [
-      "ct",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        15,
-      ],
-      "DP4": [
-        0,
-        0,
-        5,
-        6,
-      ],
-      "FQ": [
-        -67.5,
-      ],
-      "INDEL": true,
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3858,
-    "QUAL": 160,
-    "REF": "ctt",
-    "aliases": undefined,
-    "description": "deletion ctt -> ct",
-    "end": 3860,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          63,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          201,
-          33,
-          0,
-        ],
-      },
-    },
-    "start": 3857,
-    "type": "deletion",
-    "uniqueId": "test-vcf-604887",
-  },
-]
-`;

package/src/VcfTabixAdapter/configSchema.ts

@@ -1,43 +0,0 @@
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config VcfTabixAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const VcfTabixAdapter = ConfigurationSchema(
-  'VcfTabixAdapter',
-  {
-    /**
-     * #slot
-     */
-    vcfGzLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
-    },
-    index: ConfigurationSchema('VcfIndex', {
-      /**
-       * #slot index.indexType
-       */
-      indexType: {
-        model: types.enumeration('IndexType', ['TBI', 'CSI']),
-        type: 'stringEnum',
-        defaultValue: 'TBI',
-      },
-      /**
-       * #slot index.location
-       */
-      location: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.vcf.gz.tbi',
-          locationType: 'UriLocation',
-        },
-      },
-    }),
-  },
-  { explicitlyTyped: true },
-)
-
-export default VcfTabixAdapter

package/src/VcfTabixAdapter/index.ts

@@ -1,17 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export { default as configSchema } from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'VcfTabixAdapter',
-        displayName: 'VCF tabix adapter',
-        configSchema,
-        getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
-      }),
-  )
-}

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

@@ -1,20 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`plugin in a stock JBrowse 1`] = `{}`;
-
-exports[`plugin in a stock JBrowse 2`] = `
-{
-  "displays": [
-    {
-      "displayId": "trackId0-LinearVariantDisplay",
-      "type": "LinearVariantDisplay",
-    },
-    {
-      "displayId": "trackId0-ChordVariantDisplay",
-      "type": "ChordVariantDisplay",
-    },
-  ],
-  "trackId": "trackId0",
-  "type": "VariantTrack",
-}
-`;

package/src/extensionPoints.ts

@@ -1,74 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  makeIndexType,
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.vcf\.b?gz$/i
-        const adapterName = 'VcfTabixAdapter'
-        const fileName = getFileName(file)
-        const indexName = index && getFileName(index)
-        const obj = {
-          type: adapterName,
-          vcfGzLocation: file,
-          index: {
-            location: index || makeIndex(file, '.tbi'),
-            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-          },
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-  pluginManager.addToExtensionPoint(
-    'Core-guessTrackTypeForLocation',
-    (trackTypeGuesser: TrackTypeGuesser) => {
-      return (adapterName: string) => {
-        if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
-          return 'VariantTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.vcf$/i
-        const adapterName = 'VcfAdapter'
-        const fileName = getFileName(file)
-        if (regexGuess.test(fileName) || adapterHint === adapterName) {
-          return {
-            type: adapterName,
-            vcfLocation: file,
-          }
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-}

package/src/index.test.ts

@@ -1,32 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Alignments from '@jbrowse/plugin-alignments'
-import SVG from '@jbrowse/plugin-svg'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-test('plugin in a stock JBrowse', () => {
-  const pluginManager = new PluginManager([
-    new ThisPlugin(),
-    new Alignments(),
-    new SVG(),
-  ])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-
-  const VcfTabixAdapter = pluginManager.getAdapterType('VcfTabixAdapter')
-  const config = VcfTabixAdapter.configSchema.create({
-    type: 'VcfTabixAdapter',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-
-  const VariantTrack = pluginManager.getTrackType('VariantTrack')
-  const config2 = VariantTrack.configSchema.create({
-    type: 'VariantTrack',
-    trackId: 'trackId0',
-    adapter: { type: 'VcfTabixAdapter' },
-  })
-  expect(getSnapshot(config2)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,27 +0,0 @@
-import VcfAdapterF from './VcfAdapter'
-import VcfTabixAdapterF from './VcfTabixAdapter'
-import ExtensionPointsF from './extensionPoints'
-import VariantTrackF from './VariantTrack'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import ChordVariantDisplayF from './ChordVariantDisplay'
-import LinearVariantDisplayF from './LinearVariantDisplay'
-import StructuralVariantChordRendererF from './StructuralVariantChordRenderer'
-import VariantFeatureWidgetF from './VariantFeatureWidget'
-
-export default class VariantsPlugin extends Plugin {
-  name = 'VariantsPlugin'
-
-  install(pluginManager: PluginManager) {
-    VcfAdapterF(pluginManager)
-    VcfTabixAdapterF(pluginManager)
-    VariantFeatureWidgetF(pluginManager)
-    VariantTrackF(pluginManager)
-    ExtensionPointsF(pluginManager)
-    LinearVariantDisplayF(pluginManager)
-    StructuralVariantChordRendererF(pluginManager)
-    ChordVariantDisplayF(pluginManager)
-  }
-}
-
-export { default as VcfFeature } from './VcfFeature'