@jbrowse/plugin-sequence 1.7.9 → 2.0.0

package/esm/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -0,0 +1,26 @@
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class TwoBitAdapter extends BaseSequenceAdapter {
+    private twobit;
+    protected chromSizesData: Promise<Record<string, number> | undefined>;
+    private initChromSizes;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(): Promise<string[]>;
+    getRegions(): Promise<NoAssemblyRegion[]>;
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -0,0 +1,79 @@
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { TwoBitFile } from '@gmod/twobit';
+import { readConfObject } from '@jbrowse/core/configuration';
+export default class TwoBitAdapter extends BaseSequenceAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.chromSizesData = this.initChromSizes();
+        this.twobit = new TwoBitFile({
+            filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
+        });
+    }
+    async initChromSizes() {
+        const conf = readConfObject(this.config, 'chromSizesLocation');
+        // check against default and empty in case someone makes the field blank in
+        // config editor, may want better way to check "optional config slots" in
+        // future
+        if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
+            const file = openLocation(conf, this.pluginManager);
+            const data = await file.readFile('utf8');
+            return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(line => !!line.trim()).map(line => {
+                const [name, length] = line.split('\t');
+                return [name, +length];
+            }));
+        }
+        return undefined;
+    }
+    async getRefNames() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData);
+        }
+        return this.twobit.getSequenceNames();
+    }
+    async getRegions() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData).map(refName => ({
+                refName,
+                start: 0,
+                end: chromSizesData[refName],
+            }));
+        }
+        const refSizes = await this.twobit.getSequenceSizes();
+        return Object.keys(refSizes).map(refName => ({
+            refName,
+            start: 0,
+            end: refSizes[refName],
+        }));
+    }
+    /**
+     * Fetch features for a certain region
+     * @param param -
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures({ refName, start, end }) {
+        return ObservableCreate(async (observer) => {
+            const size = await this.twobit.getSequenceSize(refName);
+            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const seq = await this.twobit.getSequence(refName, start, regionEnd);
+            if (seq) {
+                observer.next(new SimpleFeature({
+                    id: `${refName} ${start}-${regionEnd}`,
+                    data: { refName, start, end: regionEnd, seq },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=TwoBitAdapter.js.map

package/esm/TwoBitAdapter/TwoBitAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAK5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,mBAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,UAAU,CAAC;YAC3B,UAAU,EAAE,YAAY,CACtB,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,IAAI,EACX,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAiBM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/esm/TwoBitAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/TwoBitAdapter/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('TwoBitAdapter', {
+    twoBitLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
+    },
+    chromSizesLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/default.chrom.sizes',
+            locationType: 'UriLocation',
+        },
+        description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/TwoBitAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/TwoBitAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/TwoBitAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/TwoBitAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class SequencePlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,197 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import Plugin from '@jbrowse/core/Plugin';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import { makeIndex, getFileName, } from '@jbrowse/core/util/tracks';
+import { configSchema as bgzipFastaAdapterConfigSchema } from './BgzipFastaAdapter';
+import { configSchema as chromSizesAdapterConfigSchema } from './ChromSizesAdapter';
+import { configSchema as divSequenceRendererConfigSchema, ReactComponent as DivSequenceRendererReactComponent, } from './DivSequenceRenderer';
+import { configSchema as indexedFastaAdapterConfigSchema } from './IndexedFastaAdapter';
+import { configSchema as linearReferenceSequenceDisplayConfigSchema, modelFactory as linearReferenceSequenceDisplayModelFactory, } from './LinearReferenceSequenceDisplay';
+import { configSchema as twoBitAdapterConfigSchema } from './TwoBitAdapter';
+import GCContentAdapterF from './GCContentAdapter';
+import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig';
+/* adjust in both directions */
+class DivSequenceRenderer extends FeatureRendererType {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    getExpandedRegion(region) {
+        return {
+            ...region,
+            start: Math.max(region.start - 3, 0),
+            end: region.end + 3,
+        };
+    }
+}
+export default class SequencePlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'SequencePlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'TwoBitAdapter',
+            configSchema: twoBitAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./TwoBitAdapter/TwoBitAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.2bit$/i;
+                const adapterName = 'TwoBitAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    twoBitLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'TwoBitAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'ChromSizesAdapter',
+            configSchema: chromSizesAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./ChromSizesAdapter/ChromSizesAdapter').then(r => r.default),
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'IndexedFastaAdapter',
+            configSchema: indexedFastaAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./IndexedFastaAdapter/IndexedFastaAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+                const adapterName = 'IndexedFastaAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    fastaLocation: file,
+                    faiLocation: index || makeIndex(file, '.fai'),
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'IndexedFastaAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'BgzipFastaAdapter',
+            configSchema: bgzipFastaAdapterConfigSchema,
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            getAdapterClass: () => import('./BgzipFastaAdapter/BgzipFastaAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+                const adapterName = 'BgzipFastaAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    faiLocation: makeIndex(file, '.fai'),
+                    gziLocation: makeIndex(file, '.gzi'),
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'BgzipFastaAdapter') {
+                    return 'ReferenceSequenceTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'GCContentAdapter',
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+            ...pluginManager.load(GCContentAdapterF),
+        }));
+        pluginManager.addTrackType(() => {
+            const configSchema = createReferenceSeqTrackConfig(pluginManager);
+            return new TrackType({
+                name: 'ReferenceSequenceTrack',
+                configSchema,
+                stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
+            });
+        });
+        pluginManager.addDisplayType(() => {
+            const stateModel = linearReferenceSequenceDisplayModelFactory(linearReferenceSequenceDisplayConfigSchema);
+            return {
+                name: 'LinearReferenceSequenceDisplay',
+                configSchema: linearReferenceSequenceDisplayConfigSchema,
+                stateModel,
+                trackType: 'ReferenceSequenceTrack',
+                viewType: 'LinearGenomeView',
+                ReactComponent: BaseLinearDisplayComponent,
+            };
+        });
+        pluginManager.addRendererType(() => new DivSequenceRenderer({
+            name: 'DivSequenceRenderer',
+            ReactComponent: DivSequenceRendererReactComponent,
+            configSchema: divSequenceRendererConfigSchema,
+            pluginManager,
+        }));
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,mBAAmB,MAAM,mEAAmE,CAAA;AACnG,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAC/E,OAAO,EACL,SAAS,EAET,WAAW,GAEZ,MAAM,2BAA2B,CAAA;AAClC,OAAO,EAAE,YAAY,IAAI,6BAA6B,EAAE,MAAM,qBAAqB,CAAA;AACnF,OAAO,EAAE,YAAY,IAAI,6BAA6B,EAAE,MAAM,qBAAqB,CAAA;AACnF,OAAO,EACL,YAAY,IAAI,+BAA+B,EAC/C,cAAc,IAAI,iCAAiC,GACpD,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,YAAY,IAAI,+BAA+B,EAAE,MAAM,uBAAuB,CAAA;AACvF,OAAO,EACL,YAAY,IAAI,0CAA0C,EAC1D,YAAY,IAAI,0CAA0C,GAC3D,MAAM,kCAAkC,CAAA;AACzC,OAAO,EAAE,YAAY,IAAI,yBAAyB,EAAE,MAAM,iBAAiB,CAAA;AAC3E,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,EAAE,6BAA6B,EAAE,MAAM,2BAA2B,CAAA;AAEzE,+BAA+B;AAC/B,MAAM,mBAAoB,SAAQ,mBAAmB;IAArD;;QACE,gBAAW,GAAG,IAAI,CAAA;IASpB,CAAC;IAPC,iBAAiB,CAAC,MAAc;QAC9B,OAAO;YACL,GAAG,MAAM;YACT,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,CAAC,CAAC;YACpC,GAAG,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC;SACpB,CAAA;IACH,CAAC;CACF;AAED,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IA0OzB,CAAC;IAxOC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,eAAe;YACrB,YAAY,EAAE,yBAAyB;YACvC,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,+BAA+B,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC/D,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,UAAU,CAAA;gBAC7B,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,eAAe,EAAE;oBACnC,OAAO,wBAAwB,CAAA;iBAChC;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,mBAAmB;YACzB,YAAY,EAAE,6BAA6B;YAC3C,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,uCAAuC,CAAC,CAAC,IAAI,CAClD,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CACf;SACJ,CAAC,CACL,CAAA;QAED,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,qBAAqB;YAC3B,YAAY,EAAE,+BAA+B;YAC7C,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,2CAA2C,CAAC,CAAC,IAAI,CACtD,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CACf;SACJ,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,4BAA4B,CAAA;gBAC/C,MAAM,WAAW,GAAG,qBAAqB,CAAA;gBACzC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,aAAa,EAAE,IAAI;oBACnB,WAAW,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;iBAC9C,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,qBAAqB,EAAE;oBACzC,OAAO,wBAAwB,CAAA;iBAChC;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,mBAAmB;YACzB,YAAY,EAAE,6BAA6B;YAC3C,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,uCAAuC,CAAC,CAAC,IAAI,CAClD,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CACf;SACJ,CAAC,CACL,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,kCAAkC,CAAA;gBACrD,MAAM,WAAW,GAAG,mBAAmB,CAAA;gBACvC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;oBACpC,WAAW,EAAE,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;iBACrC,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,mBAAmB,EAAE;oBACvC,OAAO,wBAAwB,CAAA;iBAChC;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,kBAAkB;YACxB,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,GAAG,aAAa,CAAC,IAAI,CAAC,iBAAiB,CAAC;SACzC,CAAC,CACL,CAAA;QACD,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;YAC9B,MAAM,YAAY,GAAG,6BAA6B,CAAC,aAAa,CAAC,CAAA;YAEjE,OAAO,IAAI,SAAS,CAAC;gBACnB,IAAI,EAAE,wBAAwB;gBAC9B,YAAY;gBACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;aACF,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEF,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;YAChC,MAAM,UAAU,GAAG,0CAA0C,CAC3D,0CAA0C,CAC3C,CAAA;YACD,OAAO;gBACL,IAAI,EAAE,gCAAgC;gBACtC,YAAY,EAAE,0CAA0C;gBACxD,UAAU;gBACV,SAAS,EAAE,wBAAwB;gBACnC,QAAQ,EAAE,kBAAkB;gBAC5B,cAAc,EAAE,0BAA0B;aAC3C,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,mBAAmB,CAAC;YACtB,IAAI,EAAE,qBAAqB;YAC3B,cAAc,EAAE,iCAAiC;YACjD,YAAY,EAAE,+BAA+B;YAC7C,aAAa;SACd,CAAC,CACL,CAAA;IACH,CAAC;CACF"}

package/esm/referenceSeqTrackConfig.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/referenceSeqTrackConfig.js

@@ -0,0 +1,63 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { types } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/*
+Note: this is primarily a copy of createBaseTrackConfig, except with a subset
+of the config slots, to avoid including fields that don't make sense for the
+ReferenceSequenceTrack
+*/
+export function createReferenceSeqTrackConfig(pluginManager) {
+    return ConfigurationSchema('ReferenceSequenceTrack', {
+        adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+        name: {
+            type: 'string',
+            description: 'optional track name',
+            defaultValue: '',
+        },
+        metadata: {
+            type: 'frozen',
+            description: 'anything to add about this track',
+            defaultValue: {},
+        },
+    }, {
+        preProcessSnapshot: s => {
+            const snap = JSON.parse(JSON.stringify(s));
+            const displayTypes = new Set();
+            const { displays = [] } = snap;
+            if (snap.trackId !== 'placeholderId') {
+                // Gets the displays on the track snapshot and the possible displays
+                // from the track type and adds any missing possible displays to the
+                // snapshot
+                displays.forEach((d) => d && displayTypes.add(d.type));
+                const trackType = pluginManager.getTrackType(snap.type);
+                trackType.displayTypes.forEach(displayType => {
+                    if (!displayTypes.has(displayType.name)) {
+                        displays.push({
+                            displayId: `${snap.trackId}-${displayType.name}`,
+                            type: displayType.name,
+                        });
+                    }
+                });
+            }
+            return { ...snap, displays };
+        },
+        explicitIdentifier: 'trackId',
+        explicitlyTyped: true,
+        actions: (self) => ({
+            addDisplayConf(displayConf) {
+                const { type } = displayConf;
+                if (!type) {
+                    throw new Error(`unknown display type ${type}`);
+                }
+                const display = self.displays.find((d) => d && d.displayId === displayConf.displayId);
+                if (display) {
+                    return display;
+                }
+                const length = self.displays.push(displayConf);
+                return self.displays[length - 1];
+            },
+        }),
+    });
+}
+//# sourceMappingURL=referenceSeqTrackConfig.js.map

package/esm/referenceSeqTrackConfig.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"referenceSeqTrackConfig.js","sourceRoot":"","sources":["../src/referenceSeqTrackConfig.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE;;;;EAIE;AACF,MAAM,UAAU,6BAA6B,CAAC,aAA4B;IACxE,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;KACF,EACD;QACE,kBAAkB,EAAE,CAAC,CAAC,EAAE;YACtB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,YAAY,GAAG,IAAI,GAAG,EAAE,CAAA;YAC9B,MAAM,EAAE,QAAQ,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;YAC9B,IAAI,IAAI,CAAC,OAAO,KAAK,eAAe,EAAE;gBACpC,oEAAoE;gBACpE,oEAAoE;gBACpE,WAAW;gBACX,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;gBAC3D,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACvD,SAAS,CAAC,YAAY,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE;oBAC3C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE;wBACvC,QAAQ,CAAC,IAAI,CAAC;4BACZ,SAAS,EAAE,GAAG,IAAI,CAAC,OAAO,IAAI,WAAW,CAAC,IAAI,EAAE;4BAChD,IAAI,EAAE,WAAW,CAAC,IAAI;yBACvB,CAAC,CAAA;qBACH;gBACH,CAAC,CAAC,CAAA;aACH;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,QAAQ,EAAE,CAAA;QAC9B,CAAC;QACD,kBAAkB,EAAE,SAAS;QAC7B,eAAe,EAAE,IAAI;QACrB,OAAO,EAAE,CAAC,IAAS,EAAE,EAAE,CAAC,CAAC;YACvB,cAAc,CAAC,WAAgD;gBAC7D,MAAM,EAAE,IAAI,EAAE,GAAG,WAAW,CAAA;gBAC5B,IAAI,CAAC,IAAI,EAAE;oBACT,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;iBAChD;gBACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAChC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,KAAK,WAAW,CAAC,SAAS,CACvD,CAAA;gBACD,IAAI,OAAO,EAAE;oBACX,OAAO,OAAO,CAAA;iBACf;gBACD,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC9C,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;SACF,CAAC;KACH,CACF,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.7.9",
+  "version": "2.0.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,17 +20,21 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/sequence",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -43,9 +47,10 @@
     "@jbrowse/core": "^1.0.0",
     "@jbrowse/plugin-linear-genome-view": "^1.0.0",
     "@jbrowse/plugin-wiggle": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0"
@@ -53,5 +58,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "a6504c385d703ce6e755d05652ef659ffe28c864"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

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

@@ -4,7 +4,7 @@ import { render } from '@testing-library/react'
 import { createJBrowseTheme } from '@jbrowse/core/ui'
 import PrecomputedLayout from '@jbrowse/core/util/layouts/PrecomputedLayout'
 import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import { ThemeProvider } from '@material-ui/core'
+import { ThemeProvider } from '@mui/material'
 import DivSequenceRendering from './DivSequenceRendering'
 import DivRenderingConfigSchema from '../configSchema'
 

package/src/LinearReferenceSequenceDisplay/model.ts

@@ -3,8 +3,10 @@ import {
   BaseLinearDisplay,
   LinearGenomeViewModel,
 } from '@jbrowse/plugin-linear-genome-view'
-import { ConfigurationReference } from '@jbrowse/core/configuration'
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  AnyConfigurationSchemaType,
+  ConfigurationReference,
+} from '@jbrowse/core/configuration'
 import { getContainingView } from '@jbrowse/core/util'
 
 export function modelFactory(configSchema: AnyConfigurationSchemaType) {

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.test.js

@@ -1,64 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _BgzipFastaAdapter = _interopRequireDefault(require("./BgzipFastaAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('can use a indexed fasta with gzi', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, features2, featuresArray2;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _BgzipFastaAdapter.default(_configSchema.default.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'
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context.sent;
-          expect(featuresArray).toMatchSnapshot();
-          features2 = adapter.getFeatures({
-            refName: 'ctgC',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 9;
-          return features2.pipe((0, _operators.toArray)()).toPromise();
-
-        case 9:
-          featuresArray2 = _context.sent;
-          expect(featuresArray2).toMatchSnapshot();
-
-        case 11:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/ChromSizesAdapter/ChromSizesAdapter.test.js

@@ -1,46 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _ChromSizesAdapter = _interopRequireDefault(require("./ChromSizesAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch sequence from volvox.chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, regions;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _ChromSizesAdapter.default(_configSchema.default.create({
-            chromSizesLocation: {
-              localPath: require.resolve('./test_data/volvox.chrom.sizes'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          _context.next = 3;
-          return adapter.getRegions();
-
-        case 3:
-          regions = _context.sent;
-          expect(regions).toEqual([{
-            refName: 'ctgA',
-            start: 0,
-            end: 50001
-          }, {
-            refName: 'ctgB',
-            start: 0,
-            end: 6079
-          }]);
-
-        case 5:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));