@jbrowse/plugin-gtf 2.5.0 → 2.6.2

package/dist/GtfAdapter/GtfAdapter.js

@@ -108,4 +108,3 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = default_1;
-//# sourceMappingURL=GtfAdapter.js.map

package/dist/GtfAdapter/configSchema.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 /**
  * #config GtfAdapter
+ * #category adapter
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const GtfAdapter = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
@@ -15,4 +16,3 @@ const GtfAdapter = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = GtfAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/GtfAdapter/index.js

@@ -6,4 +6,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = void 0;
 var configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -63,4 +63,3 @@ class GtfPlugin extends Plugin_1.default {
     }
 }
 exports.default = GtfPlugin;
-//# sourceMappingURL=index.js.map

package/dist/util.js

@@ -35,7 +35,7 @@ function featureData(data) {
             if (Array.isArray(attr) && attr.length === 1) {
                 // gtf uses double quotes for text values in the attributes column,
                 // remove them
-                attr = `${attr[0]}`.replace(/^"|"$/g, '');
+                attr = `${attr[0]}`.replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
         }
@@ -61,4 +61,3 @@ function featureData(data) {
     return f;
 }
 exports.featureData = featureData;
-//# sourceMappingURL=util.js.map

package/esm/GtfAdapter/GtfAdapter.js

@@ -102,4 +102,3 @@ export default class extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=GtfAdapter.js.map

package/esm/GtfAdapter/configSchema.js

@@ -1,6 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config GtfAdapter
+ * #category adapter
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const GtfAdapter = ConfigurationSchema('GtfAdapter', {
@@ -13,4 +14,3 @@ const GtfAdapter = ConfigurationSchema('GtfAdapter', {
     },
 }, { explicitlyTyped: true });
 export default GtfAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/GtfAdapter/index.js

@@ -1,2 +1 @@
 export { default as configSchema } from './configSchema';
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -34,4 +34,3 @@ export default class GtfPlugin extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/esm/util.js

@@ -32,7 +32,7 @@ export function featureData(data) {
             if (Array.isArray(attr) && attr.length === 1) {
                 // gtf uses double quotes for text values in the attributes column,
                 // remove them
-                attr = `${attr[0]}`.replace(/^"|"$/g, '');
+                attr = `${attr[0]}`.replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
         }
@@ -57,4 +57,3 @@ export function featureData(data) {
     }
     return f;
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.5.0",
+  "version": "2.6.2",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,13 +32,13 @@
     "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": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/gtf": "^0.0.6"
+    "@gmod/gtf": "^0.0.8"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -57,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/GtfAdapter/GtfAdapter.js.map

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

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package/dist/GtfAdapter/index.js.map

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package/dist/index.js.map

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package/dist/util.js.map

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package/esm/GtfAdapter/GtfAdapter.js.map

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package/esm/GtfAdapter/configSchema.js.map

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package/esm/GtfAdapter/index.js.map

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package/esm/index.js.map

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package/esm/util.js.map

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package/src/GtfAdapter/GtfAdapter.test.ts

@@ -1,55 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import configSchema from './configSchema'
-import GtfAdapter from './GtfAdapter'
-
-describe('adapter can fetch features from volvox.sorted.gtf', () => {
-  let adapter: GtfAdapter
-  beforeEach(() => {
-    adapter = new GtfAdapter(
-      configSchema.create({
-        gtfLocation: {
-          localPath: require.resolve('../test_data/volvox.sorted.gtf'),
-        },
-      }),
-    )
-  })
-  it('test getfeatures on gtf plain text adapter', async () => {
-    const features = adapter.getFeatures({
-      refName: 'ctgA',
-      start: 0,
-      end: 100000,
-    })
-    expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-    expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-    const featuresArray = await firstValueFrom(features.pipe(toArray()))
-    // There are only 4 features in ctgB
-    expect(featuresArray.length).toBe(6)
-    const featuresJsonArray = featuresArray.map(f => f.toJSON())
-    expect(featuresJsonArray).toMatchSnapshot()
-  })
-})
-
-test('can instantiate new GtfAdapter and check for demo data', async () => {
-  const demoAdapter = new GtfAdapter(
-    configSchema.create({
-      gtfLocation: {
-        localPath: require.resolve('../test_data/demo.gtf'),
-      },
-    }),
-  )
-  expect(await demoAdapter.hasDataForRefName('GeneScaffold_1')).toBe(true)
-  expect(await demoAdapter.hasDataForRefName('GeneScaffold_10')).toBe(true)
-  expect(await demoAdapter.hasDataForRefName('GeneScaffold_11')).toBe(false)
-
-  const features = demoAdapter.getFeatures({
-    refName: 'GeneScaffold_1',
-    start: 0,
-    end: 1100000,
-  })
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  // ENSVPAT00000000407
-  expect(featuresArray.length).toEqual(1)
-  expect(featuresJsonArray).toMatchSnapshot()
-})

package/src/GtfAdapter/GtfAdapter.ts

@@ -1,130 +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'
-import { unzip } from '@gmod/bgzf-filehandle'
-import gtf from '@gmod/gtf'
-
-// locals
-import { FeatureLoc, featureData } from '../util'
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class extends BaseFeatureDataAdapter {
-  protected gtfFeatures?: Promise<{
-    feats: { [key: string]: string[] }
-  }>
-
-  protected intervalTrees: {
-    [key: string]: Promise<IntervalTree | undefined> | undefined
-  } = {}
-
-  private async loadDataP(opts: BaseOptions = {}) {
-    const gtfLoc = this.getConf('gtfLocation')
-    const buffer = await openLocation(gtfLoc, this.pluginManager).readFile(opts)
-
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    // 512MB  max chrome string length is 512MB
-    if (buf.length > 536_870_888) {
-      throw new Error('Data exceeds maximum string length (512MB)')
-    }
-    const data = new TextDecoder('utf8', { fatal: true }).decode(buf)
-
-    const lines = data
-      .split(/\n|\r\n|\r/)
-      .filter(f => !!f && !f.startsWith('#'))
-    const feats = {} as { [key: string]: string[] }
-    for (let i = 0; i < lines.length; i++) {
-      const line = lines[i]
-      if (line.startsWith('#')) {
-        continue
-      }
-      const tab = line.indexOf('\t')
-      const refName = line.slice(0, tab)
-      if (!feats[refName]) {
-        feats[refName] = []
-      }
-      feats[refName].push(lines[i])
-    }
-
-    return { feats }
-  }
-
-  private async loadData(opts: BaseOptions = {}) {
-    if (!this.gtfFeatures) {
-      this.gtfFeatures = this.loadDataP(opts).catch(e => {
-        this.gtfFeatures = undefined
-        throw e
-      })
-    }
-
-    return this.gtfFeatures
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    const { feats } = await this.loadData(opts)
-    return Object.keys(feats)
-  }
-
-  private async loadFeatureIntervalTreeHelper(refName: string) {
-    const { feats } = await this.loadData()
-    const lines = feats[refName]
-    if (!lines) {
-      return undefined
-    }
-    const data = gtf.parseStringSync(lines.join('\n'), {
-      parseFeatures: true,
-      parseComments: false,
-      parseDirectives: false,
-      parseSequences: false,
-    }) as FeatureLoc[][]
-
-    const intervalTree = new IntervalTree()
-    const ret = data.flat().map(
-      (f, i) =>
-        new SimpleFeature({
-          data: featureData(f),
-          id: `${this.id}-${refName}-${i}`,
-        }),
-    )
-
-    for (let i = 0; i < ret.length; i++) {
-      const obj = ret[i]
-      intervalTree.insert([obj.get('start'), obj.get('end')], obj)
-    }
-    return intervalTree
-  }
-
-  private async loadFeatureIntervalTree(refName: string) {
-    if (!this.intervalTrees[refName]) {
-      this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(
-        refName,
-      ).catch(e => {
-        this.intervalTrees[refName] = undefined
-        throw e
-      })
-    }
-    return this.intervalTrees[refName]
-  }
-
-  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      try {
-        const { start, end, refName } = query
-        const intervalTree = await this.loadFeatureIntervalTree(refName)
-        intervalTree?.search([start, end]).forEach(f => observer.next(f))
-        observer.complete()
-      } catch (e) {
-        observer.error(e)
-      }
-    }, opts.signal)
-  }
-  public freeResources(/* { region } */) {}
-}