@jbrowse/plugin-sequence 3.6.5 → 4.0.0

package/esm/LinearReferenceSequenceDisplay/model.js

@@ -1,9 +1,9 @@
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { getContainingTrack, getContainingView } from '@jbrowse/core/util';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import { autorun } from 'mobx';
-import { addDisposer, types } from 'mobx-state-tree';
 export function modelFactory(configSchema) {
     return types
         .compose('LinearReferenceSequenceDisplay', BaseLinearDisplay, types.model({
@@ -81,7 +81,7 @@ export function modelFactory(configSchema) {
             self.showTranslation = !self.showTranslation;
         },
         afterAttach() {
-            addDisposer(self, autorun(() => {
+            addDisposer(self, autorun(function sequenceHeightAutorun() {
                 const view = getContainingView(self);
                 if (view.bpPerPx > 3) {
                     self.setHeight(50);
@@ -89,7 +89,7 @@ export function modelFactory(configSchema) {
                 else {
                     self.setHeight(self.sequenceHeight);
                 }
-            }));
+            }, { name: 'SequenceHeight' }));
         },
     }))
         .views(self => ({
@@ -125,5 +125,17 @@ export function modelFactory(configSchema) {
                     : []),
             ];
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { showForward, showReverse, showTranslation, ...rest } = snap;
+        return {
+            ...rest,
+            ...(!showForward ? { showForward } : {}),
+            ...(!showReverse ? { showReverse } : {}),
+            ...(!showTranslation ? { showTranslation } : {}),
+        };
+    });
 }

package/esm/ReferenceSequenceTrack/configSchema.d.ts

@@ -1,7 +1,7 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    adapter: import("mobx-state-tree").IAnyModelType;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
     name: {
         type: string;
         description: string;
@@ -22,7 +22,7 @@ export declare function createReferenceSeqTrackConfig(pluginManager: PluginManag
         description: string;
         defaultValue: {};
     };
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -33,5 +33,5 @@ export declare function createReferenceSeqTrackConfig(pluginManager: PluginManag
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 export function createReferenceSeqTrackConfig(pluginManager) {
     return ConfigurationSchema('ReferenceSequenceTrack', {
@@ -49,7 +49,7 @@ export function createReferenceSeqTrackConfig(pluginManager) {
                     }
                 }
                 const trackType = pluginManager.getTrackType(snap.type);
-                for (const displayType of (trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes) || []) {
+                for (const displayType of trackType?.displayTypes || []) {
                     if (!displayTypes.has(displayType.name)) {
                         displays.push({
                             displayId: `${snap.trackId}-${displayType.name}`,
@@ -68,7 +68,7 @@ export function createReferenceSeqTrackConfig(pluginManager) {
                 if (!type) {
                     throw new Error(`unknown display type ${type}`);
                 }
-                const display = self.displays.find((d) => d && d.displayId === displayConf.displayId);
+                const display = self.displays.find((d) => d?.displayId === displayConf.displayId);
                 if (display) {
                     return display;
                 }

package/esm/ReferenceSequenceTrack/index.js

@@ -1,6 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
-import { createReferenceSeqTrackConfig } from './configSchema';
+import { createReferenceSeqTrackConfig } from "./configSchema.js";
+import { stringifyFASTA } from "../saveTrackFormats/fasta.js";
 export default function ReferenceSequenceTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = createReferenceSeqTrackConfig(pluginManager);
@@ -8,7 +9,17 @@ export default function ReferenceSequenceTrackF(pluginManager) {
             name: 'ReferenceSequenceTrack',
             displayName: 'Reference sequence track',
             configSchema,
-            stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
+            stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema).views(() => ({
+                saveTrackFileFormatOptions() {
+                    return {
+                        fasta: {
+                            name: 'FASTA',
+                            extension: 'fa',
+                            callback: stringifyFASTA,
+                        },
+                    };
+                },
+            })),
         });
     });
 }

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -1,8 +1,8 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
-    configure(): Promise<BaseFeatureDataAdapter>;
+    configure(): Promise<BaseSequenceAdapter>;
     getRefNames(): Promise<string[]>;
     getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -1,12 +1,9 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, doesIntersect2, revcom } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { firstValueFrom } from 'rxjs';
-import { toArray } from 'rxjs/operators';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     async configure() {
-        var _a;
-        const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
+        const adapter = await this.getSubAdapter?.(this.getConf('sequenceAdapter'));
         if (!adapter) {
             throw new Error('Error getting subadapter');
         }
@@ -18,7 +15,6 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts) {
         return ObservableCreate(async (observer) => {
-            var _a;
             const sequenceAdapter = await this.configure();
             const hw = 10000;
             const queryEnd = query.end + hw;
@@ -27,13 +23,11 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
                 observer.complete();
                 return;
             }
-            const ret = sequenceAdapter.getFeatures({
+            const residues = (await sequenceAdapter.getSequence({
                 ...query,
                 start: queryStart,
                 end: queryEnd,
-            }, opts);
-            const feats = await firstValueFrom(ret.pipe(toArray()));
-            const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
+            }, opts)) ?? '';
             const search = this.getConf('search');
             const searchForward = this.getConf('searchForward');
             const searchReverse = this.getConf('searchReverse');

package/esm/SequenceSearchAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     search: {
         type: string;
         defaultValue: string;
@@ -20,5 +20,5 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         type: string;
         defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/SequenceSearchAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function SequenceSearchAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -9,7 +9,7 @@ export default function SequenceSearchAdapterF(pluginManager) {
                 hiddenFromGUI: true,
             },
             configSchema,
-            getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
+            getAdapterClass: () => import("./SequenceSearchAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -5,6 +5,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 export default class TwoBitAdapter extends BaseSequenceAdapter {
+    setupP;
     async initChromSizes() {
         const conf = readConfObject(this.config, 'chromSizesLocation');
         if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {

package/esm/TwoBitAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const TwoBitAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     twoBitLocation: {
         type: string;
         defaultValue: {
@@ -14,5 +14,5 @@ declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSc
         };
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default TwoBitAdapter;

package/esm/TwoBitAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function TwoBitAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'TwoBitAdapter',
@@ -8,6 +8,6 @@ export default function TwoBitAdapterF(pluginManager) {
         adapterMetadata: {
             hiddenFromGUI: true,
         },
-        getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
+        getAdapterClass: () => import("./TwoBitAdapter.js").then(r => r.default),
     }));
 }

package/esm/UnindexedFastaAdapter/UnindexedFastaAdapter.js

@@ -21,6 +21,7 @@ function parseSmallFasta(text) {
     }));
 }
 export default class UnindexedFastaAdapter extends BaseSequenceAdapter {
+    setupP;
     async getRefNames(opts) {
         const { fasta } = await this.setup(opts);
         return [...fasta.keys()];

package/esm/UnindexedFastaAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const UnindexedFastaAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     rewriteRefNames: {
         type: string;
         defaultValue: string;
@@ -19,5 +19,5 @@ declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configu
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default UnindexedFastaAdapter;

package/esm/UnindexedFastaAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function UnindexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -9,7 +9,7 @@ export default function UnindexedFastaAdapterF(pluginManager) {
             adapterMetadata: {
                 hiddenFromGUI: true,
             },
-            getAdapterClass: () => import('./UnindexedFastaAdapter').then(r => r.default),
+            getAdapterClass: () => import("./UnindexedFastaAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/index.js

@@ -1,19 +1,16 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BgzipFastaAdapterF from './BgzipFastaAdapter';
-import ChromSizesAdapterF from './ChromSizesAdapter';
-import DivSequenceRendererF from './DivSequenceRenderer';
-import IndexedFastaAdapterF from './IndexedFastaAdapter';
-import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay';
-import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
-import SequenceSearchAdapterF from './SequenceSearchAdapter';
-import TwoBitAdapterF from './TwoBitAdapter';
-import UnindexedFastaAdapterF from './UnindexedFastaAdapter';
-import createExtensionPoints from './createExtensionPoints';
+import BgzipFastaAdapterF from "./BgzipFastaAdapter/index.js";
+import ChromSizesAdapterF from "./ChromSizesAdapter/index.js";
+import DivSequenceRendererF from "./DivSequenceRenderer/index.js";
+import IndexedFastaAdapterF from "./IndexedFastaAdapter/index.js";
+import LinearReferenceSequenceDisplayF from "./LinearReferenceSequenceDisplay/index.js";
+import ReferenceSequenceTrackF from "./ReferenceSequenceTrack/index.js";
+import SequenceSearchAdapterF from "./SequenceSearchAdapter/index.js";
+import TwoBitAdapterF from "./TwoBitAdapter/index.js";
+import UnindexedFastaAdapterF from "./UnindexedFastaAdapter/index.js";
+import createExtensionPoints from "./createExtensionPoints.js";
 export default class SequencePlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'SequencePlugin';
-    }
+    name = 'SequencePlugin';
     install(pluginManager) {
         DivSequenceRendererF(pluginManager);
         TwoBitAdapterF(pluginManager);

package/esm/saveTrackFormats/fasta.d.ts

@@ -0,0 +1,4 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function stringifyFASTA({ features }: {
+    features: Feature[];
+}): string;

package/esm/saveTrackFormats/fasta.js

@@ -0,0 +1,13 @@
+export function stringifyFASTA({ features }) {
+    return features
+        .map(feature => {
+        const refName = feature.get('refName');
+        const start = Math.floor(feature.get('start'));
+        const end = Math.floor(feature.get('end'));
+        const seq = feature.get('seq') ?? '';
+        const header = `>${refName}:${start + 1}-${end}`;
+        const wrappedSeq = seq.match(/.{1,80}/g)?.join('\n') ?? '';
+        return `${header}\n${wrappedSeq}`;
+    })
+        .join('\n');
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -15,38 +15,21 @@
     "directory": "plugins/sequence"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/sequence",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/abortable-promise-cache": "^3.0.1",
-    "@gmod/indexedfasta": "^4.0.0",
-    "@gmod/twobit": "^6.0.0",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@jbrowse/plugin-wiggle": "^3.6.5",
-    "@mui/material": "^7.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "@gmod/abortable-promise-cache": "^3.0.4",
+    "@gmod/indexedfasta": "^5.0.0",
+    "@gmod/twobit": "^6.0.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.6",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "rxjs": "^7.8.2",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -54,8 +37,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/sequence",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,7 +0,0 @@
-import { BgzipIndexedFasta } from '@gmod/indexedfasta';
-import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class BgzipFastaAdapter extends IndexedFasta {
-    setupPre(): Promise<{
-        fasta: BgzipIndexedFasta;
-    }>;
-}

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,22 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const indexedfasta_1 = require("@gmod/indexedfasta");
-const io_1 = require("@jbrowse/core/util/io");
-const IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
-class BgzipFastaAdapter extends IndexedFastaAdapter_1.default {
-    async setupPre() {
-        const fastaLocation = this.getConf('fastaLocation');
-        const faiLocation = this.getConf('faiLocation');
-        const gziLocation = this.getConf('gziLocation');
-        const fastaOpts = {
-            fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
-            fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
-            gzi: (0, io_1.openLocation)(gziLocation, this.pluginManager),
-        };
-        return { fasta: new indexedfasta_1.BgzipIndexedFasta(fastaOpts) };
-    }
-}
-exports.default = BgzipFastaAdapter;

package/dist/BgzipFastaAdapter/configSchema.d.ts

@@ -1,32 +0,0 @@
-declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    fastaLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    faiLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    metadataLocation: {
-        description: string;
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    gziLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BgzipFastaAdapter;

package/dist/BgzipFastaAdapter/configSchema.js

@@ -1,54 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter', {
-    fastaLocation: {
-        type: 'fileLocation',
-        defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
-    },
-    faiLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/seq.fa.gz.fai',
-            locationType: 'UriLocation',
-        },
-    },
-    metadataLocation: {
-        description: 'Optional metadata file',
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/fa.metadata.yaml',
-            locationType: 'UriLocation',
-        },
-    },
-    gziLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/seq.fa.gz.gzi',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                fastaLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                faiLocation: {
-                    uri: `${snap.uri}.fai`,
-                    baseUri: snap.baseUri,
-                },
-                gziLocation: {
-                    uri: `${snap.uri}.gzi`,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BgzipFastaAdapter;

package/dist/BgzipFastaAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function BgzipFastaAdapterF(pluginManager: PluginManager): void;

package/dist/BgzipFastaAdapter/index.js

@@ -1,54 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = BgzipFastaAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BgzipFastaAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'BgzipFastaAdapter',
-            displayName: 'Bgzip-indexed FASTA adapter',
-            configSchema: configSchema_1.default,
-            adapterMetadata: {
-                hiddenFromGUI: true,
-            },
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,15 +0,0 @@
-import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class ChromSizesAdapter extends BaseAdapter implements RegionsAdapter {
-    protected setupP?: Promise<Record<string, number>>;
-    setupPre(): Promise<{
-        [k: string]: number;
-    }>;
-    setup(): Promise<Record<string, number>>;
-    getRegions(): Promise<{
-        refName: string;
-        start: number;
-        end: number;
-    }[]>;
-    getHeader(): {};
-}