@jbrowse/plugin-bed 2.0.0 → 2.1.2

package/dist/BigBedAdapter/BigBedAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,uDAAuD;AACvD,mCAAkC;AAClC,oDAA2B;AAC3B,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,8CAA8C;AAC9C,+DAA4D;AAC5D,kCAAiD;AAEjD,SAAS,MAAM,CAAC,CAAU;IACxB,OAAO,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;AAC5E,CAAC;AAED,MAAqB,aAAc,SAAQ,oCAAsB;IAGxD,KAAK,CAAC,YAAY,CAAC,IAAkB;QAC1C,MAAM,MAAM,GAAG,IAAI,YAAM,CAAC;YACxB,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,gBAAgB,CAAC,EAC7C,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC3C,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,OAAO,EAAE,CAAC,CAAA;QACnD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IACnC,CAAC;IAEM,KAAK,CAAC,SAAS,CAAC,IAAkB;QACvC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAA;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,CAAC,OAAO,CAAA;QAC1C,OAAO;YACL,OAAO;YACP,QAAQ;YACR,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,IAAI;gBACF,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;gBACrD,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;oBAC5D,MAAM;oBACN,YAAY,EAAE,GAAG,GAAG,KAAK;iBAC1B,CAAC,CAAA;gBACF,EAAE,CAAC,IAAI,CACL,IAAA,oBAAQ,GAAE,EACV,IAAA,eAAG,EAAC,CAAC,CAAC,EAAE;oBACN,MAAM,IAAI,GAAG,MAAM,CAAC,SAAS,CAC3B,GAAG,OAAO,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,IAAI,EAAE,EAC7C;wBACE,QAAQ,EAAE,CAAC,CAAC,QAAkB;qBAC/B,CACF,CAAA;oBAED,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBACjE,IAAI,UAAU,EAAE;wBACd,MAAM,MAAM,GAAG,WAAW,IAAI,WAAW,IAAI,EAAE,CAAA;wBAC/C,MAAM,KAAK,GAAG,UAAU,CAAA;wBACxB,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAA;wBAC5B,IAAI,CAAC,WAAW,GAAG,EAAE,CAAA;wBAErB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;4BACtC,MAAM,IAAI,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;4BAC5C,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;4BACnC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;gCACpB,QAAQ,EAAE,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,EAAE;gCAC9B,KAAK,EAAE,IAAI;gCACX,GAAG,EAAE,IAAI;gCACT,IAAI,EAAE,OAAO;6BACd,CAAC,CAAA;yBACH;qBACF;oBACD,IAAI,CAAC,CAAC,QAAQ,KAAK,SAAS,EAAE;wBAC5B,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;qBACvC;oBACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;oBAErD,MAAM,CAAC,GAAG,IAAI,uBAAa,CAAC;wBAC1B,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,QAAQ,EAAE;wBAC9B,IAAI,EAAE;4BACJ,GAAG,IAAI;4BACP,KAAK,EAAE,CAAC,CAAC,KAAK;4BACd,GAAG,EAAE,CAAC,CAAC,GAAG;4BACV,OAAO;yBACR;qBACF,CAAC,CAAA;oBAEF,4DAA4D;oBAC5D,+DAA+D;oBAC/D,6DAA6D;oBAC7D,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAA,8BAAuB,EAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACnD,CAAC,CAAC,CACH,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;aACtB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;CAChC;AA9GD,gCA8GC"}

package/dist/BigBedAdapter/configSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.default = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
     bigBedLocation: {
         type: 'fileLocation',

package/dist/BigBedAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/index.js

@@ -1,19 +1,4 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -41,35 +26,29 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var BigBedAdapter_1 = require("./BigBedAdapter");
-var BedTabixAdapter_1 = require("./BedTabixAdapter");
-var BedAdapter_1 = require("./BedAdapter");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var BedPlugin = /** @class */ (function (_super) {
-    __extends(BedPlugin, _super);
-    function BedPlugin() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'BedPlugin';
-        return _this;
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const BigBedAdapter_1 = require("./BigBedAdapter");
+const BedTabixAdapter_1 = require("./BedTabixAdapter");
+const BedAdapter_1 = require("./BedAdapter");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+class BedPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'BedPlugin';
     }
-    BedPlugin.prototype.install = function (pluginManager) {
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'BigBedAdapter',
-                configSchema: BigBedAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./BigBedAdapter/BigBedAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.(bb|bigbed)$/i;
-                var adapterName = 'BigBedAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var obj = {
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'BigBedAdapter',
+            configSchema: BigBedAdapter_1.configSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter/BigBedAdapter'))).then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(bb|bigbed)$/i;
+                const adapterName = 'BigBedAdapter';
+                const fileName = (0, tracks_1.getFileName)(file);
+                const obj = {
                     type: adapterName,
                     bigBedLocation: file,
                 };
@@ -82,30 +61,22 @@ var BedPlugin = /** @class */ (function (_super) {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'BedTabixAdapter',
-                configSchema: BedTabixAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./BedTabixAdapter/BedTabixAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'BedAdapter',
-                configSchema: BedAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./BedAdapter/BedAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.bed\.b?gz$/i;
-                var adapterName = 'BedTabixAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var indexName = index && (0, tracks_1.getFileName)(index);
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'BedTabixAdapter',
+            configSchema: BedTabixAdapter_1.configSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter/BedTabixAdapter'))).then(r => r.default),
+        }));
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'BedAdapter',
+            configSchema: BedAdapter_1.configSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter/BedAdapter'))).then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.bed\.b?gz$/i;
+                const adapterName = 'BedTabixAdapter';
+                const fileName = (0, tracks_1.getFileName)(file);
+                const indexName = index && (0, tracks_1.getFileName)(index);
                 if (regexGuess.test(fileName) || adapterHint === adapterName) {
                     return {
                         type: adapterName,
@@ -119,11 +90,11 @@ var BedPlugin = /** @class */ (function (_super) {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.bed$/i;
-                var adapterName = 'BedAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.bed$/i;
+                const adapterName = 'BedAdapter';
+                const fileName = (0, tracks_1.getFileName)(file);
                 if (regexGuess.test(fileName) || adapterHint === adapterName) {
                     return {
                         type: adapterName,
@@ -133,8 +104,7 @@ var BedPlugin = /** @class */ (function (_super) {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
-    };
-    return BedPlugin;
-}(Plugin_1.default));
+    }
+}
 exports.default = BedPlugin;
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/util.d.ts

@@ -1,4 +1,4 @@
 import { SimpleFeature, Feature } from '@jbrowse/core/util';
 import BED from '@gmod/bed';
 export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: typeof BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;
+export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;

package/dist/util.js

@@ -1,108 +1,97 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = exports.ucscProcessedTranscript = void 0;
-var util_1 = require("@jbrowse/core/util");
+const util_1 = require("@jbrowse/core/util");
 function ucscProcessedTranscript(feature) {
-    var children = feature.children();
+    const children = feature.children();
     // split the blocks into UTR, CDS, and exons
-    var thickStart = feature.get('thickStart');
-    var thickEnd = feature.get('thickEnd');
+    const thickStart = feature.get('thickStart');
+    const thickEnd = feature.get('thickEnd');
     if (!thickStart && !thickEnd) {
         return feature;
     }
-    var blocks = children
+    const blocks = children
         ? children
-            .filter(function (child) { return child.get('type') === 'block'; })
-            .sort(function (a, b) { return a.get('start') - b.get('start'); })
+            .filter(child => child.get('type') === 'block')
+            .sort((a, b) => a.get('start') - b.get('start'))
         : [];
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    var newChildren = [];
-    blocks.forEach(function (block) {
-        var start = block.get('start');
-        var end = block.get('end');
+    const newChildren = [];
+    blocks.forEach(block => {
+        const start = block.get('start');
+        const end = block.get('end');
         if (thickStart >= end) {
             // left-side UTR
-            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            const prime = feature.get('strand') > 0 ? 'five' : 'three';
             newChildren.push({
-                type: "".concat(prime, "_prime_UTR"),
-                start: start,
-                end: end,
+                type: `${prime}_prime_UTR`,
+                start,
+                end,
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd >= end) {
             // UTR | CDS
-            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            const prime = feature.get('strand') > 0 ? 'five' : 'three';
             newChildren.push({
-                type: "".concat(prime, "_prime_UTR"),
-                start: start,
+                type: `${prime}_prime_UTR`,
+                start,
                 end: thickStart,
             }, {
                 type: 'CDS',
                 start: thickStart,
-                end: end,
+                end,
             });
         }
         else if (thickStart <= start && thickEnd >= end) {
             // CDS
             newChildren.push({
                 type: 'CDS',
-                start: start,
-                end: end,
+                start,
+                end,
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd < end) {
             // UTR | CDS | UTR
-            var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
-            var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
+            const leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
+            const rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
             newChildren.push({
-                type: "".concat(leftPrime, "_prime_UTR"),
-                start: start,
+                type: `${leftPrime}_prime_UTR`,
+                start,
                 end: thickStart,
             }, {
-                type: "CDS",
+                type: `CDS`,
                 start: thickStart,
                 end: thickEnd,
             }, {
-                type: "".concat(rightPrime, "_prime_UTR"),
+                type: `${rightPrime}_prime_UTR`,
                 start: thickEnd,
-                end: end,
+                end,
             });
         }
         else if (thickStart <= start && thickEnd > start && thickEnd < end) {
             // CDS | UTR
-            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            const prime = feature.get('strand') > 0 ? 'three' : 'five';
             newChildren.push({
-                type: "CDS",
-                start: start,
+                type: `CDS`,
+                start,
                 end: thickEnd,
             }, {
-                type: "".concat(prime, "_prime_UTR"),
+                type: `${prime}_prime_UTR`,
                 start: thickEnd,
-                end: end,
+                end,
             });
         }
         else if (thickEnd <= start) {
             // right-side UTR
-            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            const prime = feature.get('strand') > 0 ? 'three' : 'five';
             newChildren.push({
-                type: "".concat(prime, "_prime_UTR"),
-                start: start,
-                end: end,
+                type: `${prime}_prime_UTR`,
+                start,
+                end,
             });
         }
     });
-    var newData = Object.fromEntries(feature.tags().map(function (tag) { return [tag, feature.get(tag)]; }));
+    const newData = Object.fromEntries(feature.tags().map(tag => [tag, feature.get(tag)]));
     newData.subfeatures = newChildren;
     newData.type = 'mRNA';
     newData.uniqueId = feature.id();
@@ -115,7 +104,7 @@ function ucscProcessedTranscript(feature) {
     delete newData.blockCount;
     delete newData.thickStart;
     delete newData.thickEnd;
-    var newFeature = new util_1.SimpleFeature({
+    const newFeature = new util_1.SimpleFeature({
         data: newData,
         id: feature.id(),
     });
@@ -123,28 +112,28 @@ function ucscProcessedTranscript(feature) {
 }
 exports.ucscProcessedTranscript = ucscProcessedTranscript;
 function defaultParser(fields, line) {
-    return Object.fromEntries(line.split('\t').map(function (f, i) { return [fields[i], f]; }));
+    return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
 }
 function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
-    var l = line.split('\t');
-    var refName = l[colRef];
-    var start = +l[colStart];
-    var colSame = colStart === colEnd ? 1 : 0;
-    var end = +l[colEnd] + colSame;
-    var data = names
+    const l = line.split('\t');
+    const refName = l[colRef];
+    const start = +l[colStart];
+    const colSame = colStart === colEnd ? 1 : 0;
+    const end = +l[colEnd] + colSame;
+    const data = names
         ? defaultParser(names, line)
-        : parser.parseLine(line, { uniqueId: uniqueId });
-    var blockCount = data.blockCount, blockSizes = data.blockSizes, blockStarts = data.blockStarts, chromStarts = data.chromStarts;
+        : parser.parseLine(line, { uniqueId });
+    const { blockCount, blockSizes, blockStarts, chromStarts } = data;
     if (blockCount) {
-        var starts = chromStarts || blockStarts || [];
-        var sizes = blockSizes;
-        var blocksOffset = start;
+        const starts = chromStarts || blockStarts || [];
+        const sizes = blockSizes;
+        const blocksOffset = start;
         data.subfeatures = [];
-        for (var b = 0; b < blockCount; b += 1) {
-            var bmin = (starts[b] || 0) + blocksOffset;
-            var bmax = bmin + (sizes[b] || 0);
+        for (let b = 0; b < blockCount; b += 1) {
+            const bmin = (starts[b] || 0) + blocksOffset;
+            const bmax = bmin + (sizes[b] || 0);
             data.subfeatures.push({
-                uniqueId: "".concat(uniqueId, "-").concat(b),
+                uniqueId: `${uniqueId}-${b}`,
                 start: bmin,
                 end: bmax,
                 type: 'block',
@@ -157,7 +146,13 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
     delete data.chrom;
     delete data.chromStart;
     delete data.chromEnd;
-    var f = new util_1.SimpleFeature(__assign(__assign({}, data), { start: start, end: end, refName: refName, uniqueId: uniqueId }));
+    const f = new util_1.SimpleFeature({
+        ...data,
+        start,
+        end,
+        refName,
+        uniqueId,
+    });
     return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
 }
 exports.featureData = featureData;

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/BedAdapter/BedAdapter.d.ts

@@ -6,7 +6,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     protected bedFeatures?: Promise<{
         header: string;
         features: Record<string, string[]>;
-        parser: typeof BED;
+        parser: BED;
         columnNames: string[];
         scoreColumn: string;
         colRef: number;

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';

package/esm/BedTabixAdapter/BedTabixAdapter.js.map

@@ -1 +1 @@
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package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,35 +1,19 @@
 import { BigBed } from '@gmod/bbi';
+import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-interface BEDFeature {
-    chrom: string;
-    chromStart: number;
-    chromEnd: number;
-    [key: string]: any;
-}
-interface Parser {
-    parseLine: (line: string, opts: {
-        uniqueId: string | number;
-    }) => BEDFeature;
-    autoSql: {
-        fields: {
-            name: string;
-            comment: string;
-        }[];
-    };
-}
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cached?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: any;
-        parser: Parser;
+        header: import("@gmod/bbi").Header;
+        parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
         header: any;
-        parser: Parser;
+        parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<{
@@ -43,4 +27,3 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }
-export {};

package/esm/BigBedAdapter/BigBedAdapter.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -1,4 +1,4 @@
 import { SimpleFeature, Feature } from '@jbrowse/core/util';
 import BED from '@gmod/bed';
 export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: typeof BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;
+export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;

package/esm/util.js.map

@@ -1 +1 @@
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