@jbrowse/plugin-gtf 3.6.5 → 4.0.0

package/esm/GtfAdapter/GtfAdapter.d.ts

@@ -1,15 +1,16 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 import type { Observer } from 'rxjs';
 type StatusCallback = (arg: string) => void;
+type SimpleFeat = SimpleFeatureSerialized;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    calculatedIntervalTreeMap: Record<string, IntervalTree<SimpleFeat>>;
     gtfFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<SimpleFeat>>;
     }>;
     private loadDataP;
     private loadData;

package/esm/GtfAdapter/GtfAdapter.js

@@ -1,16 +1,14 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, doesIntersect2, fetchAndMaybeUnzip, max, min, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { parseStringSync } from 'gtf-nostream';
-import { featureData } from '../util';
+import { featureData } from "../util.js";
 export default class GtfAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
+    calculatedIntervalTreeMap = {};
+    gtfFeatures;
     async loadDataP(opts) {
         const loc = openLocation(this.getConf('gtfLocation'), this.pluginManager);
         const buffer = await fetchAndMaybeUnzip(loc, opts);
@@ -32,12 +30,12 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
                 featureMap[refName] += `${line}\n`;
             }
             return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        }, opts?.statusCallback);
         const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
             refName,
             (sc) => {
                 if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
+                    sc?.('Parsing GTF data');
                     const intervalTree = new IntervalTree();
                     for (const obj of parseStringSync(lines)
                         .flat()
@@ -87,11 +85,10 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
         }, opts.stopToken);
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        var _a;
         const aggregateField = this.getConf('aggregateField');
         const { start, end, refName } = query;
         const { intervalTreeMap } = await this.loadData(opts);
-        const feats = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+        const feats = intervalTreeMap[refName]?.(opts.statusCallback).search([
             start,
             end,
         ]);
@@ -116,8 +113,8 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
                     await this.getFeaturesHelper({
                         query: {
                             ...query,
-                            start: minStart - 500000,
-                            end: maxEnd + 500000,
+                            start: minStart - 500_000,
+                            end: maxEnd + 500_000,
                         },
                         opts,
                         observer,
@@ -128,9 +125,6 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
                 }
             }
             const parentAggregation = {};
-            if (feats.some(f => f.uniqueId === undefined)) {
-                throw new Error('found uniqueId undefined');
-            }
             for (const feat of feats) {
                 const aggr = feat[aggregateField];
                 if (!parentAggregation[aggr]) {

package/esm/GtfAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const GtfAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     gtfLocation: {
         type: string;
         description: string;
@@ -12,5 +12,5 @@ declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchem
         description: string;
         defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default GtfAdapter;

package/esm/GtfAdapter/index.js

@@ -1,10 +1,10 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function GtfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'GtfAdapter',
         displayName: 'GTF adapter',
         configSchema,
-        getAdapterClass: () => import('./GtfAdapter').then(r => r.default),
+        getAdapterClass: () => import("./GtfAdapter.js").then(r => r.default),
     }));
 }

package/esm/index.js

@@ -1,11 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
-import GtfAdapterF from './GtfAdapter';
-import GuessAdapterF from './GuessAdapter';
+import GtfAdapterF from "./GtfAdapter/index.js";
+import GuessAdapterF from "./GuessAdapter/index.js";
 export default class GtfPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'GTFPlugin';
-    }
+    name = 'GTFPlugin';
     install(pluginManager) {
         GtfAdapterF(pluginManager);
         GuessAdapterF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -15,37 +15,21 @@
     "directory": "plugins/gtf"
   },
   "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/gtf --passWithNoTests",
-    "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": {
-    "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@mui/material": "^7.0.0",
-    "gtf-nostream": "^1.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "@flatten-js/interval-tree": "^2.0.3",
+    "@gmod/bgzf-filehandle": "^6.0.9",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.6",
+    "gtf-nostream": "^1.3.4",
+    "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"
@@ -53,8 +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/gtf --passWithNoTests",
+    "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/GtfAdapter/GtfAdapter.d.ts

@@ -1,27 +0,0 @@
-import IntervalTree from '@flatten-js/interval-tree';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util';
-import type { Region } from '@jbrowse/core/util/types';
-import type { Observer } from 'rxjs';
-type StatusCallback = (arg: string) => void;
-export default class GtfAdapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
-    gtfFeatures?: Promise<{
-        header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
-    }>;
-    private loadDataP;
-    private loadData;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
-        query: Region;
-        opts: BaseOptions;
-        observer: Observer<Feature>;
-        allowRedispatch: boolean;
-        originalQuery?: Region;
-    }): Promise<void>;
-}
-export {};

package/dist/GtfAdapter/GtfAdapter.js

@@ -1,177 +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 interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const gtf_nostream_1 = require("gtf-nostream");
-const util_2 = require("../util");
-class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
-    async loadDataP(opts) {
-        const loc = (0, io_1.openLocation)(this.getConf('gtfLocation'), this.pluginManager);
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        const headerLines = [];
-        const featureMap = {};
-        (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-            if (line.startsWith('#')) {
-                headerLines.push(line);
-            }
-            else if (line.startsWith('>')) {
-                return false;
-            }
-            else {
-                const ret = line.indexOf('\t');
-                const refName = line.slice(0, ret);
-                if (!featureMap[refName]) {
-                    featureMap[refName] = '';
-                }
-                featureMap[refName] += `${line}\n`;
-            }
-            return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
-            refName,
-            (sc) => {
-                if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
-                    const intervalTree = new interval_tree_1.default();
-                    for (const obj of (0, gtf_nostream_1.parseStringSync)(lines)
-                        .flat()
-                        .map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}`))) {
-                        intervalTree.insert([obj.start, obj.end], obj);
-                    }
-                    this.calculatedIntervalTreeMap[refName] = intervalTree;
-                }
-                return this.calculatedIntervalTreeMap[refName];
-            },
-        ]));
-        return {
-            header: headerLines.join('\n'),
-            intervalTreeMap,
-        };
-    }
-    async loadData(opts = {}) {
-        if (!this.gtfFeatures) {
-            this.gtfFeatures = this.loadDataP(opts).catch((e) => {
-                this.gtfFeatures = undefined;
-                throw e;
-            });
-        }
-        return this.gtfFeatures;
-    }
-    async getRefNames(opts = {}) {
-        const { intervalTreeMap } = await this.loadData(opts);
-        return Object.keys(intervalTreeMap);
-    }
-    async getHeader(opts = {}) {
-        const { header } = await this.loadData(opts);
-        return header;
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            try {
-                await this.getFeaturesHelper({
-                    query,
-                    opts,
-                    observer,
-                    allowRedispatch: true,
-                });
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        }, opts.stopToken);
-    }
-    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        var _a;
-        const aggregateField = this.getConf('aggregateField');
-        const { start, end, refName } = query;
-        const { intervalTreeMap } = await this.loadData(opts);
-        const feats = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
-            start,
-            end,
-        ]);
-        if (feats) {
-            if (allowRedispatch && feats.length) {
-                let minStart = Number.POSITIVE_INFINITY;
-                let maxEnd = Number.NEGATIVE_INFINITY;
-                let hasAnyAggregateField = false;
-                for (const feat of feats) {
-                    if (feat.start < minStart) {
-                        minStart = feat.start;
-                    }
-                    if (feat.end > maxEnd) {
-                        maxEnd = feat.end;
-                    }
-                    if (feat[aggregateField]) {
-                        hasAnyAggregateField = true;
-                    }
-                }
-                if (hasAnyAggregateField &&
-                    (maxEnd > query.end || minStart < query.start)) {
-                    await this.getFeaturesHelper({
-                        query: {
-                            ...query,
-                            start: minStart - 500000,
-                            end: maxEnd + 500000,
-                        },
-                        opts,
-                        observer,
-                        allowRedispatch: false,
-                        originalQuery: query,
-                    });
-                    return;
-                }
-            }
-            const parentAggregation = {};
-            if (feats.some(f => f.uniqueId === undefined)) {
-                throw new Error('found uniqueId undefined');
-            }
-            for (const feat of feats) {
-                const aggr = feat[aggregateField];
-                if (!parentAggregation[aggr]) {
-                    parentAggregation[aggr] = [];
-                }
-                if (aggr) {
-                    parentAggregation[aggr].push(feat);
-                }
-                else {
-                    observer.next(new util_1.SimpleFeature({
-                        id: feat.uniqueId,
-                        data: feat,
-                    }));
-                }
-            }
-            for (const [name, subfeatures] of Object.entries(parentAggregation)) {
-                const s = (0, util_1.min)(subfeatures.map(f => f.start));
-                const e = (0, util_1.max)(subfeatures.map(f => f.end));
-                if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
-                    const { uniqueId, strand } = subfeatures[0];
-                    observer.next(new util_1.SimpleFeature({
-                        id: `${uniqueId}-parent`,
-                        data: {
-                            type: 'gene',
-                            subfeatures,
-                            strand,
-                            name,
-                            start: s,
-                            end: e,
-                            refName: query.refName,
-                        },
-                    }));
-                }
-            }
-        }
-        observer.complete();
-    }
-}
-exports.default = GtfAdapter;

package/dist/GtfAdapter/configSchema.d.ts

@@ -1,16 +0,0 @@
-declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    gtfLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    aggregateField: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default GtfAdapter;

package/dist/GtfAdapter/configSchema.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const GtfAdapter = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
-    gtfLocation: {
-        type: 'fileLocation',
-        description: 'path to gtf file, also allows for gzipped gtf',
-        defaultValue: {
-            uri: '/path/to/my.gtf',
-            locationType: 'UriLocation',
-        },
-    },
-    aggregateField: {
-        type: 'string',
-        description: 'field used to aggregate multiple transcripts into a single parent gene feature',
-        defaultValue: 'gene_name',
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                gtfLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = GtfAdapter;

package/dist/GtfAdapter/index.d.ts

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

package/dist/GtfAdapter/index.js

@@ -1,49 +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 = GtfAdapterF;
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function GtfAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
-        name: 'GtfAdapter',
-        displayName: 'GTF adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GtfAdapter'))).then(r => r.default),
-    }));
-}

package/dist/GuessAdapter/index.d.ts

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

package/dist/GuessAdapter/index.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessAdapterF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessAdapterF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            return (0, util_1.testAdapter)(fileName, /\.gtf(\.gz)?$/i, adapterHint, 'GtfAdapter')
-                ? {
-                    type: 'GtfAdapter',
-                    gtfLocation: file,
-                }
-                : adapterGuesser(file, index, adapterHint);
-        };
-    });
-}

package/dist/index.d.ts

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

package/dist/index.js

@@ -1,19 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const GtfAdapter_1 = __importDefault(require("./GtfAdapter"));
-const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
-class GtfPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'GTFPlugin';
-    }
-    install(pluginManager) {
-        (0, GtfAdapter_1.default)(pluginManager);
-        (0, GuessAdapter_1.default)(pluginManager);
-    }
-}
-exports.default = GtfPlugin;

package/dist/util.d.ts

@@ -1,13 +0,0 @@
-export type Strand = '+' | '-' | '.' | '?';
-export interface FeatureLoc {
-    [key: string]: unknown;
-    start: number;
-    end: number;
-    strand: Strand;
-    seq_name: string;
-    child_features?: FeatureLoc[][];
-    data: unknown;
-    derived_features: unknown;
-    attributes: Record<string, unknown[]>;
-}
-export declare function featureData(data: FeatureLoc, id?: string): Record<string, unknown>;

package/dist/util.js

@@ -1,59 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = featureData;
-function featureData(data, id) {
-    const f = { ...data };
-    f.start -= 1;
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
-    f.phase = Number(data.frame);
-    f.refName = data.seq_name;
-    if (data.score === null) {
-        f.score = undefined;
-    }
-    if (data.frame === null) {
-        f.score = undefined;
-    }
-    const defaultFields = new Set([
-        'start',
-        'end',
-        'seq_name',
-        'score',
-        'featureType',
-        'source',
-        'frame',
-        'strand',
-    ]);
-    for (const a of Object.keys(data.attributes)) {
-        let b = a.toLowerCase();
-        if (defaultFields.has(b)) {
-            b += '2';
-        }
-        if (data.attributes[a]) {
-            let attr = data.attributes[a];
-            if (Array.isArray(attr) && attr.length === 1) {
-                attr = attr[0].replaceAll(/^"|"$/g, '');
-            }
-            f[b] = attr;
-        }
-    }
-    f.refName = f.seq_name;
-    f.type = f.featureType;
-    if (data.child_features && data.child_features.length > 0) {
-        f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
-    }
-    f.child_features = undefined;
-    f.data = undefined;
-    f.derived_features = undefined;
-    f._linehash = undefined;
-    f.attributes = undefined;
-    f.seq_name = undefined;
-    f.featureType = undefined;
-    f.frame = undefined;
-    if (f.transcript_id) {
-        f.name = f.transcript_id;
-    }
-    if (id !== undefined) {
-        f.uniqueId = id;
-    }
-    return f;
-}