@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/CramAdapter/CramTestAdapters.js

@@ -1,176 +1,79 @@
 "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 __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SequenceAdapter = exports.FetchableSmallFasta = exports.parseSmallFasta = void 0;
-var rxjs_1 = require("rxjs");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var configurationSchema_1 = require("@jbrowse/core/configuration/configurationSchema");
+const rxjs_1 = require("rxjs");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const configurationSchema_1 = require("@jbrowse/core/configuration/configurationSchema");
 // setup for Cram Adapter Testing
 function parseSmallFasta(text) {
     return text
         .split('>')
-        .filter(function (t) { return /\S/.test(t); })
-        .map(function (entryText) {
-        var _a = __read(entryText.split('\n')), defLine = _a[0], seqLines = _a.slice(1);
-        var _b = __read(defLine.split(' ')), id = _b[0], descriptionLines = _b.slice(1);
-        var description = descriptionLines.join(' ');
-        var sequence = seqLines.join('').replace(/\s/g, '');
-        return { id: id, description: description, sequence: sequence };
+        .filter(t => /\S/.test(t))
+        .map(entryText => {
+        const [defLine, ...seqLines] = entryText.split('\n');
+        const [id, ...descriptionLines] = defLine.split(' ');
+        const description = descriptionLines.join(' ');
+        const sequence = seqLines.join('').replace(/\s/g, '');
+        return { id, description, sequence };
     });
 }
 exports.parseSmallFasta = parseSmallFasta;
-var FetchableSmallFasta = /** @class */ (function () {
-    function FetchableSmallFasta(filehandle) {
-        this.data = filehandle.readFile().then(function (buffer) {
-            var text = buffer.toString('utf8');
+class FetchableSmallFasta {
+    constructor(filehandle) {
+        this.data = filehandle.readFile().then(buffer => {
+            const text = buffer.toString('utf8');
             return parseSmallFasta(text);
         });
     }
-    FetchableSmallFasta.prototype.fetch = function (id, start, end) {
-        return __awaiter(this, void 0, void 0, function () {
-            var data, entry, length;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.data];
-                    case 1:
-                        data = _a.sent();
-                        entry = data[id];
-                        length = end - start + 1;
-                        if (!entry) {
-                            throw new Error("no sequence with id ".concat(id, " exists"));
-                        }
-                        return [2 /*return*/, entry.sequence.substr(start - 1, length)];
-                }
-            });
-        });
-    };
-    FetchableSmallFasta.prototype.getSequenceList = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var data;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.data];
-                    case 1:
-                        data = _a.sent();
-                        return [2 /*return*/, data.map(function (entry) { return entry.id; })];
-                }
-            });
-        });
-    };
-    return FetchableSmallFasta;
-}());
+    async fetch(id, start, end) {
+        const data = await this.data;
+        const entry = data[id];
+        const length = end - start + 1;
+        if (!entry) {
+            throw new Error(`no sequence with id ${id} exists`);
+        }
+        return entry.sequence.substr(start - 1, length);
+    }
+    async getSequenceList() {
+        const data = await this.data;
+        return data.map(entry => entry.id);
+    }
+}
 exports.FetchableSmallFasta = FetchableSmallFasta;
-var SequenceAdapter = /** @class */ (function (_super) {
-    __extends(SequenceAdapter, _super);
-    function SequenceAdapter(filehandle) {
-        var _this = _super.call(this, (0, configurationSchema_1.ConfigurationSchema)('empty', {}).create()) || this;
-        _this.refNames = [];
-        _this.fasta = new FetchableSmallFasta(filehandle);
-        return _this;
+class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor(filehandle) {
+        super((0, configurationSchema_1.ConfigurationSchema)('empty', {}).create());
+        this.refNames = [];
+        this.fasta = new FetchableSmallFasta(filehandle);
     }
-    SequenceAdapter.prototype.getRefNames = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                return [2 /*return*/, this.refNames];
-            });
-        });
-    };
-    SequenceAdapter.prototype.getFeatures = function (_a) {
-        var _this = this;
-        var refName = _a.refName, start = _a.start, end = _a.end;
-        return new rxjs_1.Observable(function (observer) {
-            _this.fasta
+    async getRefNames() {
+        return this.refNames;
+    }
+    getFeatures({ refName, start, end, }) {
+        return new rxjs_1.Observable(observer => {
+            this.fasta
                 .getSequenceList()
-                .then(function (refNames) {
-                _this.refNames = refNames;
-            })
-                .then(function () {
-                return _this.fasta.fetch(_this.refNames.indexOf(refName), start, end);
+                .then(refNames => {
+                this.refNames = refNames;
             })
-                .then(function (ret) {
+                .then(() => this.fasta.fetch(this.refNames.indexOf(refName), start, end))
+                .then(ret => {
                 observer.next(new simpleFeature_1.default({
-                    uniqueId: "".concat(refName, "-").concat(start, "-").concat(end),
+                    uniqueId: `${refName}-${start}-${end}`,
                     seq: ret,
-                    start: start,
-                    end: end,
+                    start,
+                    end,
                 }));
                 observer.complete();
             });
-            return { unsubscribe: function () { } };
+            return { unsubscribe: () => { } };
         });
-    };
-    SequenceAdapter.prototype.freeResources = function ( /* { region } */) { };
-    return SequenceAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+    }
+    freeResources( /* { region } */) { }
+}
 exports.SequenceAdapter = SequenceAdapter;
 //# sourceMappingURL=CramTestAdapters.js.map

package/dist/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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package/dist/CramAdapter/configSchema.js

@@ -1,30 +1,28 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = (function (pluginManager) {
-    return mobx_state_tree_1.types.late(function () {
-        return (0, configuration_1.ConfigurationSchema)('CramAdapter', {
-            fetchSizeLimit: {
-                type: 'number',
-                defaultValue: 3000000,
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (pluginManager) => {
+    return mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('CramAdapter', {
+        fetchSizeLimit: {
+            type: 'number',
+            defaultValue: 3000000,
+        },
+        cramLocation: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.cram',
+                locationType: 'UriLocation',
             },
-            cramLocation: {
-                type: 'fileLocation',
-                defaultValue: {
-                    uri: '/path/to/my.cram',
-                    locationType: 'UriLocation',
-                },
+        },
+        craiLocation: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.cram.crai',
+                locationType: 'UriLocation',
             },
-            craiLocation: {
-                type: 'fileLocation',
-                defaultValue: {
-                    uri: '/path/to/my.cram.crai',
-                    locationType: 'UriLocation',
-                },
-            },
-            sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        }, { explicitlyTyped: true });
-    });
-});
+        },
+        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    }, { explicitlyTyped: true }));
+};
 //# sourceMappingURL=configSchema.js.map

package/dist/CramAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AACA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,OAAO,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACrB,IAAA,mCAAmB,EACjB,aAAa,EACb;QACE,cAAc,EAAE;YACd,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,OAAS;SACxB;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,kBAAkB;gBACvB,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,uBAAuB;gBAC5B,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA;AACH,CAAC,CAAA"}

package/dist/CramAdapter/index.js

@@ -26,16 +26,14 @@ 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"));
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 // locals
-var configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (function (pluginManager) {
-    pluginManager.addAdapterType(function () {
-        return new AdapterType_1.default({
-            name: 'CramAdapter',
-            configSchema: pluginManager.load(configSchema_1.default),
-            getAdapterClass: function () { return Promise.resolve().then(function () { return __importStar(require('./CramAdapter')); }).then(function (r) { return r.default; }); },
-        });
-    });
-});
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'CramAdapter',
+        configSchema: pluginManager.load(configSchema_1.default),
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/CramAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,sBAAa,CAAC;QAC/C,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -1,95 +1,33 @@
 "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 __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var bam_1 = require("@gmod/bam");
-var configuration_1 = require("@jbrowse/core/configuration");
-var BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
-var HtsgetBamAdapter = /** @class */ (function (_super) {
-    __extends(HtsgetBamAdapter, _super);
-    function HtsgetBamAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    HtsgetBamAdapter.prototype.configure = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var htsgetBase, htsgetTrackId, bam_2, adapterConfig;
-            return __generator(this, function (_a) {
-                if (!this.configured) {
-                    htsgetBase = (0, configuration_1.readConfObject)(this.config, 'htsgetBase');
-                    htsgetTrackId = (0, configuration_1.readConfObject)(this.config, 'htsgetTrackId');
-                    bam_2 = new bam_1.HtsgetFile({
-                        baseUrl: htsgetBase,
-                        trackId: htsgetTrackId,
-                    });
-                    adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-                    if (adapterConfig && this.getSubAdapter) {
-                        this.configured = this.getSubAdapter(adapterConfig).then(function (_a) {
-                            var dataAdapter = _a.dataAdapter;
-                            return {
-                                bam: bam_2,
-                                sequenceAdapter: dataAdapter,
-                            };
-                        });
-                    }
-                    this.configured = Promise.resolve({ bam: bam_2 });
-                }
-                return [2 /*return*/, this.configured];
+const bam_1 = require("@gmod/bam");
+const configuration_1 = require("@jbrowse/core/configuration");
+const BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
+class HtsgetBamAdapter extends BamAdapter_1.default {
+    async configure() {
+        if (!this.configured) {
+            const htsgetBase = (0, configuration_1.readConfObject)(this.config, 'htsgetBase');
+            const htsgetTrackId = (0, configuration_1.readConfObject)(this.config, 'htsgetTrackId');
+            const bam = new bam_1.HtsgetFile({
+                baseUrl: htsgetBase,
+                trackId: htsgetTrackId,
             });
-        });
-    };
-    return HtsgetBamAdapter;
-}(BamAdapter_1.default));
+            const adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
+            if (adapterConfig && this.getSubAdapter) {
+                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => {
+                    return {
+                        bam,
+                        sequenceAdapter: dataAdapter,
+                    };
+                });
+            }
+            this.configured = Promise.resolve({ bam });
+        }
+        return this.configured;
+    }
+}
 exports.default = HtsgetBamAdapter;
 //# sourceMappingURL=HtsgetBamAdapter.js.map

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA+C;AAC/C,6DAA4D;AAE5D,wEAAiD;AAEjD;IAA8C,oCAAU;IAAxD;;IAyBA,CAAC;IAxBiB,oCAAS,GAAzB;;;;gBACE,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;oBACd,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;oBACtD,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;oBAC5D,QAAM,IAAI,gBAAU,CAAC;wBACzB,OAAO,EAAE,UAAU;wBACnB,OAAO,EAAE,aAAa;qBACvB,CAAuB,CAAA;oBAElB,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;oBACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;wBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,UAAC,EAAe;gCAAb,WAAW,iBAAA;4BACZ,OAAO;gCACL,GAAG,OAAA;gCACH,eAAe,EAAE,WAAqC;6BACvD,CAAA;wBACH,CAAC,CACF,CAAA;qBACF;oBACD,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,OAAA,EAAE,CAAC,CAAA;iBAC3C;gBACD,sBAAO,IAAI,CAAC,UAAU,EAAA;;;KACvB;IACH,uBAAC;AAAD,CAAC,AAzBD,CAA8C,oBAAU,GAyBvD"}
+{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAA+C;AAC/C,+DAA4D;AAE5D,0EAAiD;AAEjD,MAAqB,gBAAiB,SAAQ,oBAAU;IAC5C,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;YAC5D,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;YAClE,MAAM,GAAG,GAAG,IAAI,gBAAU,CAAC;gBACzB,OAAO,EAAE,UAAU;gBACnB,OAAO,EAAE,aAAa;aACvB,CAAuB,CAAA;YAExB,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;YACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;gBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,CAAC,EAAE,WAAW,EAAE,EAAE,EAAE;oBAClB,OAAO;wBACL,GAAG;wBACH,eAAe,EAAE,WAAqC;qBACvD,CAAA;gBACH,CAAC,CACF,CAAA;aACF;YACD,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;SAC3C;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;CACF;AAzBD,mCAyBC"}

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,21 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = mobx_state_tree_1.types.late(function () {
-    return (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
-        htsgetBase: {
-            type: 'string',
-            defaultValue: '',
-        },
-        htsgetTrackId: {
-            type: 'string',
-            defaultValue: '',
-        },
-        sequenceAdapter: {
-            type: 'frozen',
-            defaultValue: null,
-        },
-    }, { explicitlyTyped: true });
-});
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
+    htsgetBase: {
+        type: 'string',
+        defaultValue: '',
+    },
+    htsgetTrackId: {
+        type: 'string',
+        defaultValue: '',
+    },
+    sequenceAdapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true }));
 //# sourceMappingURL=configSchema.js.map

package/dist/HtsgetBamAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,mDAAuC;AAEvC,kBAAe,uBAAK,CAAC,IAAI,CAAC;IACxB,OAAA,IAAA,mCAAmB,EACjB,kBAAkB,EAClB;QACE,UAAU,EAAE;YACV,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,EAAE;SACjB;QACD,aAAa,EAAE;YACb,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,EAAE;SACjB;QACD,eAAe,EAAE;YACf,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,IAAI;SACnB;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B;AAjBD,CAiBC,CACF,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CAC7B,IAAA,mCAAmB,EACjB,kBAAkB,EAClB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}

package/dist/HtsgetBamAdapter/index.js

@@ -26,23 +26,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var configSchema_1 = __importDefault(require("./configSchema"));
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-exports.default = (function (pluginManager) {
-    pluginManager.addAdapterType(function () {
-        return new AdapterType_1.default({
-            name: 'HtsgetBamAdapter',
-            adapterMetadata: {
-                category: null,
-                hiddenFromGUI: true,
-                displayName: null,
-                description: null,
-            },
-            configSchema: configSchema_1.default,
-            getAdapterClass: function () {
-                return Promise.resolve().then(function () { return __importStar(require('./HtsgetBamAdapter')); }).then(function (r) { return r.default; });
-            },
-        });
-    });
-});
+const configSchema_1 = __importDefault(require("./configSchema"));
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'HtsgetBamAdapter',
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/HtsgetBamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gEAAyC;AAEzC,gGAAyE;AAEzE,mBAAe,UAAC,aAA4B;IAC1C,aAAa,CAAC,cAAc,CAC1B;QACE,OAAA,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,kBAAkB;YACxB,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;gBACjB,WAAW,EAAE,IAAI;aAClB;YACD,YAAY,wBAAA;YACZ,eAAe,EAAE;gBACf,OAAA,iEAAO,oBAAoB,OAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,EAAT,CAAS,CAAC;YAAjD,CAAiD;SACpD,CAAC;IAXF,CAWE,CACL,CAAA;AACH,CAAC,EAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,kGAAyE;AAEzE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -3,32 +3,31 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var mobx_react_1 = require("mobx-react");
-var configuration_1 = require("@jbrowse/core/configuration");
-var ui_1 = require("@jbrowse/core/ui");
-var mui_1 = require("tss-react/mui");
-var useStyles = (0, mui_1.makeStyles)()(function () { return ({
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const ui_1 = require("@jbrowse/core/ui");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(() => ({
     resizeHandle: {
         height: 2,
         position: 'absolute',
         zIndex: 2,
     },
-}); });
-function AlignmentsDisplay(_a) {
-    var model = _a.model;
-    var PileupDisplay = model.PileupDisplay, SNPCoverageDisplay = model.SNPCoverageDisplay, showPileup = model.showPileup, showCoverage = model.showCoverage;
-    var classes = useStyles().classes;
-    var top = SNPCoverageDisplay.height;
-    return (react_1.default.createElement("div", { "data-testid": "display-".concat((0, configuration_1.getConf)(model, 'displayId')), style: { position: 'relative' } },
+}));
+function AlignmentsDisplay({ model }) {
+    const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model;
+    const { classes } = useStyles();
+    const top = SNPCoverageDisplay.height;
+    return (react_1.default.createElement("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' } },
         showCoverage ? (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement("div", { "data-testid": "Blockset-snpcoverage" },
                 react_1.default.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-            react_1.default.createElement(ui_1.ResizeHandle, { onDrag: function (delta) {
+            react_1.default.createElement(ui_1.ResizeHandle, { onDrag: delta => {
                     SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
                     return delta;
                 }, className: classes.resizeHandle, style: {
-                    top: top,
+                    top,
                 } }))) : null,
         showPileup ? (react_1.default.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',