@jbrowse/plugin-bed 2.17.0 → 3.0.0

package/dist/BedGraphTabixAdapter/configSchema.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
+const BedGraphTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphTabixAdapter', {
+    bedGraphGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
+        indexType: {
+            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.vcf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+exports.default = BedGraphTabixAdapter;

package/dist/BedGraphTabixAdapter/index.d.ts

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

package/dist/BedGraphTabixAdapter/index.js

@@ -0,0 +1,49 @@
+"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 = BedGraphTabixAdapterF;
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function BedGraphTabixAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'BedGraphTabixAdapter',
+        displayName: 'BedGraphTabix adapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedGraphTabixAdapter'))).then(r => r.default),
+    }));
+}

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,9 +1,10 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     private parser;
     protected bed: TabixIndexedFile;

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -4,12 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bed_1 = __importDefault(require("@gmod/bed"));
+const tabix_1 = require("@gmod/tabix");
 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 rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
-const tabix_1 = require("@gmod/tabix");
-// locals
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const util_2 = require("../util");
 class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -50,6 +50,7 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             : undefined;
     }
     getFeatures(query, opts = {}) {
+        const { stopToken } = opts;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const meta = await this.bed.getMetadata();
             const { columnNumbers } = meta;
@@ -57,8 +58,14 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
             const names = await this.getNames();
+            let start = performance.now();
+            (0, stopToken_1.checkStopToken)(stopToken);
             await this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
+                    if (performance.now() - start > 200) {
+                        (0, stopToken_1.checkStopToken)(stopToken);
+                        start = performance.now();
+                    }
                     observer.next(new util_1.SimpleFeature((0, util_2.featureData)({
                         line,
                         colRef,
@@ -70,10 +77,10 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                         names,
                     })));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BedTabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,25 +20,16 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     autoSql: {
         type: string;
         description: string;

package/dist/BedTabixAdapter/configSchema.js

@@ -2,30 +2,18 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config BedTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -34,25 +22,16 @@ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapte
             },
         },
     }),
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     autoSql: {
         type: 'string',
         description: 'The autoSql definition for the data fields in the file',

package/dist/BedTabixAdapter/index.d.ts

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

package/dist/BedTabixAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,7 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature, SimpleFeature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
-export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -3,76 +3,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = featureData;
+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 rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
-function featureData(line, uniqueId, flip, names) {
-    const l = line.split('\t');
-    const ref1 = l[flip ? 3 : 0];
-    const start1 = +l[flip ? 4 : 1];
-    const end1 = +l[flip ? 5 : 2];
-    const ref2 = l[!flip ? 3 : 0];
-    const start2 = +l[!flip ? 4 : 1];
-    const end2 = +l[!flip ? 5 : 2];
-    const name = l[6];
-    const score = +l[7];
-    const strand1 = parseStrand(l[8]);
-    const strand2 = parseStrand(l[9]);
-    const extra = l.slice(10);
-    const rest = names
-        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-        : extra;
-    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
-    return new util_1.SimpleFeature({
-        ...rest,
-        start: start1,
-        end: end1,
-        type: 'paired_feature',
-        refName: ref1,
-        strand: strand1,
-        name,
-        score,
-        uniqueId,
-        mate: {
-            refName: ref2,
-            start: start2,
-            end: end2,
-            strand: strand2,
-        },
-        ...(ALT ? { ALT: [ALT] } : {}), // ALT is an array in VCF
-    });
-}
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    if (strand === '-') {
-        return -1;
-    }
-    if (strand === '.') {
-        return 0;
-    }
-    return undefined;
-}
+const util_2 = require("./util");
 class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.intervalTrees = {};
     }
     async loadDataP(opts) {
-        const pm = this.pluginManager;
-        const bedLoc = this.getConf('bedpeLocation');
-        const loc = (0, io_1.openLocation)(bedLoc, pm);
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        // 512MB  max chrome string length is 512MB
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const data = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(this.getConf('bedpeLocation'), this.pluginManager), opts);
         const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
         const headerLines = [];
         let i = 0;
@@ -140,8 +83,8 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { feats1, feats2 } = await this.loadData();
         const names = await this.getNames();
         const intervalTree = new interval_tree_1.default();
-        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
-        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
+        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
+        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
         for (const obj of [...ret1, ...ret2]) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);
         }
@@ -164,7 +107,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BedpeAdapter/configSchema.d.ts

@@ -1,8 +1,4 @@
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +6,6 @@ declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;

package/dist/BedpeAdapter/configSchema.js

@@ -1,16 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BedpeAdapter
- * intended for SVs in a single assembly
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -18,9 +10,6 @@ const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',

package/dist/BedpeAdapter/index.d.ts

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

package/dist/BedpeAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/BedpeAdapter/util.d.ts

@@ -0,0 +1,2 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;

package/dist/BedpeAdapter/util.js

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = featureData;
+const util_1 = require("@jbrowse/core/util");
+const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
+function featureData(line, uniqueId, flip, names) {
+    const l = line.split('\t');
+    const ref1 = l[flip ? 3 : 0];
+    const start1 = +l[flip ? 4 : 1];
+    const end1 = +l[flip ? 5 : 2];
+    const ref2 = l[!flip ? 3 : 0];
+    const start2 = +l[!flip ? 4 : 1];
+    const end2 = +l[!flip ? 5 : 2];
+    const name = l[6];
+    const score = +l[7];
+    const strand1 = parseStrand(l[8]);
+    const strand2 = parseStrand(l[9]);
+    const extra = l.slice(10);
+    const rest = names
+        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
+        : {};
+    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
+    return new util_1.SimpleFeature({
+        ...rest,
+        start: start1,
+        end: end1,
+        type: 'paired_feature',
+        refName: ref1,
+        strand: strand1,
+        name,
+        score,
+        uniqueId,
+        mate: {
+            refName: ref2,
+            start: start2,
+            end: end2,
+            strand: strand2,
+        },
+        ...(ALT ? { ALT: [ALT] } : {}),
+    });
+}
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else if (strand === '.') {
+        return 0;
+    }
+    else {
+        return undefined;
+    }
+}

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,9 +1,10 @@
 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';
-import { Observer } from 'rxjs';
+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';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -6,11 +6,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const bbi_1 = require("@gmod/bbi");
 const bed_1 = __importDefault(require("@gmod/bed"));
 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 rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
 const rxjs_2 = require("rxjs");
-// locals
 const util_2 = require("../util");
 class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre(opts) {
@@ -67,12 +66,13 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        const { signal } = opts;
+        var _a;
+        const { stopToken } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const { parser, bigbed } = await this.configure(opts);
         const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
-            signal,
+            stopToken,
             basesPerSpan: query.end - query.start,
         });
         if (allowRedispatch && feats.length) {
@@ -106,8 +106,13 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             throw new Error('found uniqueId undefined');
         }
         for (const feat of feats) {
-            const line = `${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`;
-            const data = parser.parseLine(line, { uniqueId: feat.uniqueId });
+            const splitLine = [
+                query.refName,
+                `${feat.start}`,
+                `${feat.end}`,
+                ...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
+            ];
+            const data = parser.parseLine(splitLine, { uniqueId: feat.uniqueId });
             const aggr = data[aggregateField];
             if (!parentAggregation[aggr]) {
                 parentAggregation[aggr] = [];
@@ -116,7 +121,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const f = (0, util_2.featureData2)({
                 ...rest,
                 scoreColumn,
-                line,
+                splitLine,
                 parser,
                 uniqueId,
                 start: feat.start,
@@ -169,7 +174,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }