@jbrowse/plugin-variants 2.3.2 → 2.3.3

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,14 +1,12 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-import { GenericFilehandle } from 'generic-filehandle';
 export default class extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{
-        filehandle: GenericFilehandle;
         vcf: TabixIndexedFile;
         parser: VcfParser;
     }>;
@@ -16,20 +14,5 @@ export default class extends BaseFeatureDataAdapter {
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
-const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
@@ -28,7 +27,6 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
         });
         const header = await vcf.getHeader();
         return {
-            filehandle,
             vcf,
             parser: new vcf_1.default({ header }),
         };
@@ -71,38 +69,6 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.signal);
     }
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { vcf } = await this.configure();
-            // @ts-ignore
-            const bytes = await (0, util_1.bytesForRegions)(regions, vcf.index);
-            const { filehandle } = await this.configure();
-            const stat = await filehandle.stat();
-            let pct = Math.round((bytes / stat.size) * 100);
-            if (pct > 100) {
-                // this is just a bad estimate, make 100% if it goes over
-                pct = 100;
-            }
-            if (pct > 60) {
-                console.warn(`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`);
-            }
-            super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
-        });
-    }
     freeResources( /* { region } */) { }
 }
 exports.default = default_1;

package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,oDAAiC;AAEjC,QAAQ;AACR,+DAAsC;AAEtC,eAAqB,SAAQ,oCAAsB;IAMzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,IAAA,iBAAY,EAAC,aAA6B,EAAE,EAAE,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,GAAG;YACH,MAAM,EAAE,IAAI,aAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA3ED,4BA2EC"}

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,14 +1,12 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-import { GenericFilehandle } from 'generic-filehandle';
 export default class extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{
-        filehandle: GenericFilehandle;
         vcf: TabixIndexedFile;
         parser: VcfParser;
     }>;
@@ -16,20 +14,5 @@ export default class extends BaseFeatureDataAdapter {
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,6 +1,5 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
-import { bytesForRegions } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
@@ -23,7 +22,6 @@ export default class extends BaseFeatureDataAdapter {
         });
         const header = await vcf.getHeader();
         return {
-            filehandle,
             vcf,
             parser: new VcfParser({ header }),
         };
@@ -66,38 +64,6 @@ export default class extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.signal);
     }
-    /**
-     * Checks if the data source has data for the given reference sequence,
-     * and then gets the features in the region if it does
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * Also includes a bit of extra logging to warn when fetching a large portion
-     * of a VCF
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions, opts = {}) {
-        return ObservableCreate(async (observer) => {
-            const { vcf } = await this.configure();
-            // @ts-ignore
-            const bytes = await bytesForRegions(regions, vcf.index);
-            const { filehandle } = await this.configure();
-            const stat = await filehandle.stat();
-            let pct = Math.round((bytes / stat.size) * 100);
-            if (pct > 100) {
-                // this is just a bad estimate, make 100% if it goes over
-                pct = 100;
-            }
-            if (pct > 60) {
-                console.warn(`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`);
-            }
-            super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
-        });
-    }
     freeResources( /* { region } */) { }
 }
 //# sourceMappingURL=VcfTabixAdapter.js.map

package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAMzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,YAAY,CAAC,aAA6B,EAAE,EAAE,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.3.2",
+  "version": "2.3.3",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,7 +55,7 @@
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0",
+    "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
   "publishConfig": {
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx

@@ -0,0 +1,42 @@
+import React from 'react'
+import { render } from '@testing-library/react'
+import { types } from 'mobx-state-tree'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+// locals
+import { stateModelFactory } from '.'
+import VariantFeatureDetails from './VariantFeatureWidget'
+
+test('renders with just the required model elements', () => {
+  const pluginManager = new PluginManager([])
+  const Session = types.model({
+    rpcManager: types.optional(types.frozen(), {}),
+    configuration: ConfigurationSchema('test', {}),
+    widget: stateModelFactory(pluginManager),
+  })
+  const model = Session.create(
+    {
+      widget: {
+        // @ts-ignore
+        type: 'VariantFeatureWidget',
+      },
+    },
+    { pluginManager },
+  )
+  model.widget.setFeatureData({
+    refName: 'ctgA',
+    start: 176,
+    end: 177,
+    name: 'rs123',
+    REF: 'A',
+    ALT: ['<TRA>'],
+    QUAL: 10.4,
+    INFO: {
+      MQ: 5,
+    },
+  })
+
+  const { container } = render(<VariantFeatureDetails model={model.widget} />)
+  expect(container.firstChild).toMatchSnapshot()
+})

package/src/VariantFeatureWidget/__snapshots__/{VariantFeatureWidget.test.js.snap → VariantFeatureWidget.test.tsx.snap}

@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`VariantTrack widget renders with just the required model elements 1`] = `
+exports[`renders with just the required model elements 1`] = `
 <div
   class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1ps6pg7-MuiPaper-root"
   data-testid="variant-side-drawer"

package/src/VcfAdapter/VcfAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './VcfAdapter'
 import configSchema from './configSchema'
 
@@ -12,7 +13,7 @@ test('adapter can fetch variants from volvox.vcf', async () => {
     }),
   )
 
-  const features = adapter.getFeatures({
+  const feat = adapter.getFeatures({
     assemblyName: 'volvox',
     refName: 'ctgA',
     start: 0,
@@ -22,6 +23,6 @@ test('adapter can fetch variants from volvox.vcf', async () => {
   const names = await adapter.getRefNames()
   expect(names).toMatchSnapshot()
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray.slice(0, 5)).toMatchSnapshot()
+  const featArray = await firstValueFrom(feat.pipe(toArray()))
+  expect(featArray.slice(0, 5)).toMatchSnapshot()
 })

package/src/VcfTabixAdapter/VcfTabixAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './VcfTabixAdapter'
 import configSchema from './configSchema'
 
@@ -46,25 +47,23 @@ test('adapter can fetch variants from volvox.vcf.gz', async () => {
   expect(names).toEqual(csiNames)
   expect(names).toMatchSnapshot()
 
-  const features = adapter.getFeatures({
+  const feat = adapter.getFeatures({
     refName: 'ctgA',
     start: 0,
     end: 20000,
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const csiFeaturesArray = await csiFeatures.pipe(toArray()).toPromise()
-  expect(featuresArray.slice(0, 5)).toMatchSnapshot()
-  expect(csiFeaturesArray.slice(0, 5)).toEqual(featuresArray.slice(0, 5))
+  const featArray = await firstValueFrom(feat.pipe(toArray()))
+  const csiFeaturesArray = await firstValueFrom(csiFeatures.pipe(toArray()))
+  expect(featArray.slice(0, 5)).toMatchSnapshot()
+  expect(csiFeaturesArray.slice(0, 5)).toEqual(featArray.slice(0, 5))
 
-  const featuresNonExist = adapter.getFeatures({
+  const featNonExist = adapter.getFeatures({
     refName: 'ctgC',
     start: 0,
     end: 20000,
   })
 
-  const featuresArrayNonExist = await featuresNonExist
-    .pipe(toArray())
-    .toPromise()
-  expect(featuresArrayNonExist).toEqual([])
+  const featArrayNonExist = await firstValueFrom(featNonExist.pipe(toArray()))
+  expect(featArrayNonExist).toEqual([])
 })

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -2,26 +2,18 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import {
-  FileLocation,
-  NoAssemblyRegion,
-  Region,
-} from '@jbrowse/core/util/types'
+import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { bytesForRegions } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { Feature } from '@jbrowse/core/util'
 import { TabixIndexedFile } from '@gmod/tabix'
 import VcfParser from '@gmod/vcf'
-import { Observer } from 'rxjs'
-import { GenericFilehandle } from 'generic-filehandle'
 
 // local
 import VcfFeature from '../VcfFeature'
 
 export default class extends BaseFeatureDataAdapter {
   private configured?: Promise<{
-    filehandle: GenericFilehandle
     vcf: TabixIndexedFile
     parser: VcfParser
   }>
@@ -44,7 +36,6 @@ export default class extends BaseFeatureDataAdapter {
 
     const header = await vcf.getHeader()
     return {
-      filehandle,
       vcf,
       parser: new VcfParser({ header }),
     }
@@ -95,44 +86,5 @@ export default class extends BaseFeatureDataAdapter {
     }, opts.signal)
   }
 
-  /**
-   * Checks if the data source has data for the given reference sequence,
-   * and then gets the features in the region if it does
-   *
-   * Currently this just calls getFeatureInRegion for each region. Adapters that
-   * are frequently called on multiple regions simultaneously may want to
-   * implement a more efficient custom version of this method.
-   *
-   * Also includes a bit of extra logging to warn when fetching a large portion
-   * of a VCF
-   * @param regions - Regions
-   * @param opts - Feature adapter options
-   * @returns Observable of Feature objects in the regions
-   */
-  public getFeaturesInMultipleRegions(
-    regions: Region[],
-    opts: BaseOptions = {},
-  ) {
-    return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {
-      const { vcf } = await this.configure()
-
-      // @ts-ignore
-      const bytes = await bytesForRegions(regions, vcf.index)
-      const { filehandle } = await this.configure()
-      const stat = await filehandle.stat()
-      let pct = Math.round((bytes / stat.size) * 100)
-      if (pct > 100) {
-        // this is just a bad estimate, make 100% if it goes over
-        pct = 100
-      }
-      if (pct > 60) {
-        console.warn(
-          `getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,
-        )
-      }
-      super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
-    })
-  }
-
   public freeResources(/* { region } */): void {}
 }

package/src/{index.test.js → index.test.ts}

@@ -5,7 +5,6 @@ import { getSnapshot } from 'mobx-state-tree'
 import ThisPlugin from '.'
 
 test('plugin in a stock JBrowse', () => {
-  console.warn = jest.fn()
   const pluginManager = new PluginManager([
     new ThisPlugin(),
     new Alignments(),

package/src/LinearVariantDisplay/configSchema.test.js

@@ -1,55 +0,0 @@
-import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import PileupRenderer from '@jbrowse/plugin-alignments/src/PileupRenderer'
-import {
-  configSchema as svgFeatureRendererConfigSchema,
-  ReactComponent as SvgFeatureRendererReactComponent,
-} from '@jbrowse/plugin-svg/src/SvgFeatureRenderer'
-import configSchemaFactory from './configSchema'
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(() => {
-  jest.spyOn(console, 'warn').mockImplementation(() => {})
-})
-
-afterEach(() => {
-  console.warn.mockRestore()
-})
-
-class PileupRendererPlugin extends Plugin {
-  install(pluginManager) {
-    PileupRenderer(pluginManager)
-  }
-}
-
-class SvgFeatureRendererPlugin extends Plugin {
-  install(pluginManager) {
-    pluginManager.addRendererType(
-      () =>
-        new BoxRendererType({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: SvgFeatureRendererReactComponent,
-          configSchema: svgFeatureRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-  }
-}
-
-test('has a viewType attr', () => {
-  const configSchema = configSchemaFactory(
-    new PluginManager([
-      new PileupRendererPlugin(),
-      new SvgFeatureRendererPlugin(),
-    ])
-      .createPluggableElements()
-      .configure(),
-  )
-  const config = configSchema.create({
-    type: 'LinearVariantDisplay',
-    displayId: 'displayId0',
-    name: 'Zonker Display',
-  })
-  expect(config.type).toEqual('LinearVariantDisplay')
-})

package/src/VariantFeatureWidget/VariantFeatureWidget.test.js

@@ -1,41 +0,0 @@
-import React from 'react'
-import { render } from '@testing-library/react'
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { stateModelFactory } from '.'
-
-import VariantFeatureDetails from './VariantFeatureWidget'
-
-describe('VariantTrack widget', () => {
-  it('renders with just the required model elements', () => {
-    console.warn = jest.fn()
-    const pluginManager = new PluginManager([])
-    const Session = types.model({
-      rpcManager: types.optional(types.frozen(), {}),
-      configuration: ConfigurationSchema('test', {}),
-      widget: stateModelFactory(pluginManager),
-    })
-    const model = Session.create(
-      {
-        widget: { type: 'VariantFeatureWidget' },
-      },
-      { pluginManager },
-    )
-    model.widget.setFeatureData({
-      refName: 'ctgA',
-      start: 176,
-      end: 177,
-      name: 'rs123',
-      REF: 'A',
-      ALT: ['<TRA>'],
-      QUAL: 10.4,
-      INFO: {
-        MQ: 5,
-      },
-    })
-
-    const { container } = render(<VariantFeatureDetails model={model.widget} />)
-    expect(container.firstChild).toMatchSnapshot()
-  })
-})