@jbrowse/plugin-gff3 2.6.1 → 2.6.2

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -145,4 +145,3 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = default_1;
-//# sourceMappingURL=Gff3Adapter.js.map

package/dist/Gff3Adapter/configSchema.js

@@ -16,4 +16,3 @@ const Gff3Adapter = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = Gff3Adapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/Gff3Adapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3Adapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -188,4 +188,3 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = default_1;
-//# sourceMappingURL=Gff3TabixAdapter.js.map

package/dist/Gff3TabixAdapter/configSchema.js

@@ -48,4 +48,3 @@ const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdap
     },
 }, { explicitlyTyped: true });
 exports.default = Gff3TabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/Gff3TabixAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3TabixAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/GuessGff3/index.js

@@ -41,4 +41,3 @@ exports.default = (pluginManager) => {
         };
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -19,4 +19,3 @@ class default_1 extends Plugin_1.default {
     }
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -139,4 +139,3 @@ export default class extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=Gff3Adapter.js.map

package/esm/Gff3Adapter/configSchema.js

@@ -14,4 +14,3 @@ const Gff3Adapter = ConfigurationSchema('Gff3Adapter', {
     },
 }, { explicitlyTyped: true });
 export default Gff3Adapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/Gff3Adapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -182,4 +182,3 @@ export default class extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=Gff3TabixAdapter.js.map

package/esm/Gff3TabixAdapter/configSchema.js

@@ -46,4 +46,3 @@ const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
     },
 }, { explicitlyTyped: true });
 export default Gff3TabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/Gff3TabixAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./Gff3TabixAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/GuessGff3/index.js

@@ -39,4 +39,3 @@ export default (pluginManager) => {
         };
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -13,4 +13,3 @@ export default class extends Plugin {
         GuessGff3F(pluginManager);
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -56,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/Gff3Adapter/Gff3Adapter.js.map

@@ -1 +0,0 @@
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package/dist/Gff3Adapter/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/Gff3Adapter/index.js.map

@@ -1 +0,0 @@
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package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map

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package/esm/Gff3Adapter/Gff3Adapter.js.map

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package/esm/Gff3Adapter/configSchema.js.map

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package/esm/Gff3Adapter/index.js.map

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package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map

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package/esm/Gff3TabixAdapter/configSchema.js.map

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package/esm/Gff3TabixAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/GuessGff3/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessGff3/index.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,SAAS,EACT,aAAa,EACb,WAAW,GAEZ,MAAM,2BAA2B,CAAA;AAElC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;YACpC,MAAM,WAAW,GAAG,kBAAkB,CAAA;YACtC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;YAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;gBAC5D,OAAO;oBACL,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;oBACjB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;aACF;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,WAAW,CAAA;YAC9B,MAAM,WAAW,GAAG,aAAa,CAAA;YACjC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,WAAW,EAAE,IAAI;aAClB,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}

package/esm/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,YAAY,MAAM,eAAe,CAAA;AACxC,OAAO,UAAU,MAAM,aAAa,CAAA;AAEpC,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAOrB,CAAC;IALC,OAAO,CAAC,aAA4B;QAClC,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,YAAY,CAAC,aAAa,CAAC,CAAA;QAC3B,UAAU,CAAC,aAAa,CAAC,CAAA;IAC3B,CAAC;CACF"}

package/src/Gff3Adapter/Gff3Adapter.test.ts

@@ -1,31 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import configSchema from './configSchema'
-import Gff3Adapter from './Gff3Adapter'
-
-describe('adapter can fetch features from volvox.gff3', () => {
-  let adapter: Gff3Adapter
-  beforeEach(() => {
-    adapter = new Gff3Adapter(
-      configSchema.create({
-        gffLocation: {
-          localPath: require.resolve('../test_data/volvox.sort.gff3'),
-        },
-      }),
-    )
-  })
-  it('test getfeatures on gff plain text adapter', async () => {
-    const features = adapter.getFeatures({
-      refName: 'ctgB',
-      start: 0,
-      end: 200000,
-    })
-    expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-    expect(await adapter.hasDataForRefName('ctgB')).toBe(true)
-    const featuresArray = await firstValueFrom(features.pipe(toArray()))
-    // There are only 4 features in ctgB
-    expect(featuresArray.length).toBe(4)
-    const featuresJsonArray = featuresArray.map(f => f.toJSON())
-    expect(featuresJsonArray).toMatchSnapshot()
-  })
-})

package/src/Gff3Adapter/Gff3Adapter.ts

@@ -1,166 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { openLocation } from '@jbrowse/core/util/io'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import IntervalTree from '@flatten-js/interval-tree'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { unzip } from '@gmod/bgzf-filehandle'
-
-import gff, { GFF3FeatureLineWithRefs } from '@gmod/gff'
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class extends BaseFeatureDataAdapter {
-  protected gffFeatures?: Promise<{
-    header: string
-    intervalTree: Record<string, IntervalTree>
-  }>
-
-  private async loadDataP() {
-    const pm = this.pluginManager
-    const buf = await openLocation(this.getConf('gffLocation'), pm).readFile()
-    const buffer = isGzip(buf) ? await unzip(buf) : buf
-    // 512MB  max chrome string length is 512MB
-    if (buffer.length > 536_870_888) {
-      throw new Error('Data exceeds maximum string length (512MB)')
-    }
-    const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)
-    const lines = data.split(/\n|\r\n|\r/)
-    const headerLines = []
-    for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
-      headerLines.push(lines[i])
-    }
-    const header = headerLines.join('\n')
-
-    const feats = gff.parseStringSync(data, {
-      parseFeatures: true,
-      parseComments: false,
-      parseDirectives: false,
-      parseSequences: false,
-      disableDerivesFromReferences: true,
-    })
-
-    const intervalTree = {} as Record<string, IntervalTree>
-    for (const obj of feats.flat().map(
-      (f, i) =>
-        new SimpleFeature({
-          data: this.featureData(f),
-          id: `${this.id}-offset-${i}`,
-        }),
-    )) {
-      const key = obj.get('refName')
-      if (!intervalTree[key]) {
-        intervalTree[key] = new IntervalTree()
-      }
-      intervalTree[key].insert([obj.get('start'), obj.get('end')], obj)
-    }
-
-    return { header, intervalTree }
-  }
-
-  private async loadData() {
-    if (!this.gffFeatures) {
-      this.gffFeatures = this.loadDataP().catch(e => {
-        this.gffFeatures = undefined
-        throw e
-      })
-    }
-
-    return this.gffFeatures
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    const { intervalTree } = await this.loadData()
-    return Object.keys(intervalTree)
-  }
-
-  public async getHeader() {
-    const { header } = await this.loadData()
-    return header
-  }
-
-  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      try {
-        const { start, end, refName } = query
-        const { intervalTree } = await this.loadData()
-        intervalTree[refName]
-          ?.search([start, end])
-          .forEach(f => observer.next(f))
-        observer.complete()
-      } catch (e) {
-        observer.error(e)
-      }
-    }, opts.signal)
-  }
-
-  private featureData(data: GFF3FeatureLineWithRefs) {
-    const f: Record<string, unknown> = { ...data }
-    ;(f.start as number) -= 1 // convert to interbase
-    if (data.strand === '+') {
-      f.strand = 1
-    } else if (data.strand === '-') {
-      f.strand = -1
-    } else if (data.strand === '.') {
-      f.strand = 0
-    } else {
-      f.strand = undefined
-    }
-    f.phase = Number(data.phase)
-    f.refName = data.seq_id
-    if (data.score === null) {
-      delete f.score
-    }
-    if (data.phase === null) {
-      delete f.score
-    }
-    const defaultFields = new Set([
-      'start',
-      'end',
-      'seq_id',
-      'score',
-      'type',
-      'source',
-      'phase',
-      'strand',
-    ])
-    const dataAttributes = data.attributes || {}
-    for (const a of Object.keys(dataAttributes)) {
-      let b = a.toLowerCase()
-      if (defaultFields.has(b)) {
-        // add "suffix" to tag name if it already exists
-        // reproduces behavior of NCList
-        b += '2'
-      }
-      if (dataAttributes[a] !== null) {
-        let attr: string | string[] | undefined = dataAttributes[a]
-        if (Array.isArray(attr) && attr.length === 1) {
-          ;[attr] = attr
-        }
-        f[b] = attr
-      }
-    }
-    f.refName = f.seq_id
-
-    // the SimpleFeature constructor takes care of recursively inflating subfeatures
-    if (data.child_features && data.child_features.length > 0) {
-      f.subfeatures = data.child_features.flatMap(childLocs =>
-        childLocs.map(childLoc => this.featureData(childLoc)),
-      )
-    }
-
-    delete f.child_features
-    delete f.data
-    // delete f.derived_features
-    delete f.attributes
-    delete f.seq_id
-    return f
-  }
-
-  public freeResources(/* { region } */) {}
-}

package/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap

@@ -1,57 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
-[
-  {
-    "derived_features": [],
-    "end": 6079,
-    "name": "ctgB",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 0,
-    "strand": undefined,
-    "type": "contig",
-    "uniqueId": "test-offset-187",
-  },
-  {
-    "derived_features": [],
-    "end": 1984,
-    "name": "f07",
-    "note": "This is an example",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 1658,
-    "strand": 1,
-    "type": "remark",
-    "uniqueId": "test-offset-188",
-  },
-  {
-    "derived_features": [],
-    "end": 6130,
-    "name": "f06",
-    "note": "This is another example",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 3013,
-    "strand": 1,
-    "type": "remark",
-    "uniqueId": "test-offset-189",
-  },
-  {
-    "derived_features": [],
-    "end": 5968,
-    "name": "f05",
-    "note": "ああ、この機能は、世界中を旅しています！",
-    "phase": 0,
-    "refName": "ctgB",
-    "source": "example",
-    "start": 4714,
-    "strand": -1,
-    "type": "remark",
-    "uniqueId": "test-offset-190",
-  },
-]
-`;

package/src/Gff3Adapter/configSchema.ts

@@ -1,23 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config Gff3Adapter
- * #category adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const Gff3Adapter = ConfigurationSchema(
-  'Gff3Adapter',
-  {
-    /**
-     * #slot
-     */
-    gffLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default Gff3Adapter

package/src/Gff3Adapter/index.ts

@@ -1,15 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'Gff3Adapter',
-        displayName: 'GFF3 adapter',
-        configSchema,
-        getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
-      }),
-  )
-}

package/src/Gff3TabixAdapter/Gff3TabixAdapter.test.ts

@@ -1,37 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import configSchema from './configSchema'
-import Gff3TabixAdapter from './Gff3TabixAdapter'
-
-describe('adapter can fetch features from volvox.gff3', () => {
-  let adapter: Gff3TabixAdapter
-  beforeEach(() => {
-    adapter = new Gff3TabixAdapter(
-      configSchema.create({
-        gffGzLocation: {
-          localPath: require.resolve('../test_data/volvox.sort.gff3.gz'),
-        },
-        index: {
-          location: {
-            localPath: require.resolve('../test_data/volvox.sort.gff3.gz.tbi'),
-          },
-        },
-      }),
-    )
-  })
-  it('test getfeatures on gff plain text adapter', async () => {
-    const features = adapter.getFeatures({
-      refName: 'ctgB',
-      start: 0,
-      end: 200000,
-      assemblyName: 'volvox',
-    })
-    expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-    expect(await adapter.hasDataForRefName('ctgB')).toBe(true)
-    const featuresArray = await firstValueFrom(features.pipe(toArray()))
-    // There are only 4 features in ctgB
-    expect(featuresArray.length).toBe(4)
-    const featuresJsonArray = featuresArray.map(f => f.toJSON())
-    expect(featuresJsonArray).toMatchSnapshot()
-  })
-})