@jbrowse/plugin-variants 2.0.0 → 2.1.2

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -0,0 +1,83 @@
+"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 (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;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const x_data_grid_1 = require("@mui/x-data-grid");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+function VariantSamples(props) {
+    const [filter, setFilter] = (0, react_1.useState)({});
+    const [showFilters, setShowFilters] = (0, react_1.useState)(false);
+    const { feature } = props;
+    const { samples = {} } = feature;
+    const preFilteredRows = Object.entries(samples);
+    if (!preFilteredRows.length) {
+        return null;
+    }
+    const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(field => ({
+        field,
+    }));
+    let error;
+    let rows = [];
+    const filters = Object.keys(filter);
+    // catch some error thrown from regex
+    // note: maps all values into a string, if this is not done rows are not
+    // sortable by the data-grid
+    try {
+        rows = preFilteredRows
+            .map((row) => ({
+            ...Object.fromEntries(Object.entries(row[1]).map(entry => [entry[0], String(entry[1])])),
+            sample: row[0],
+            id: row[0],
+        }))
+            .filter((row) => {
+            return filters.length
+                ? filters.every(key => {
+                    const val = row[key];
+                    const currFilter = filter[key];
+                    return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                })
+                : true;
+        });
+    }
+    catch (e) {
+        error = e;
+    }
+    // disableSelectionOnClick helps avoid
+    // https://github.com/mui-org/material-ui-x/issues/1197
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Samples" },
+        error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
+        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
+        showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+            infoFields.map(({ field }) => {
+                return (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }));
+            }))) : null,
+        react_1.default.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
+            react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }))));
+}
+exports.default = VariantSamples;
+//# sourceMappingURL=VariantSampleGrid.js.map

package/dist/VariantFeatureWidget/VariantSampleGrid.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"VariantSampleGrid.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantSampleGrid.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AAEvC,4CAKsB;AAEtB,kDAA2C;AAC3C,yFAA4E;AAE5E,SAAwB,cAAc,CAAC,KAAU;IAC/C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAM,EAAE,CAAC,CAAA;IAC7C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACrD,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAEzB,MAAM,EAAE,OAAO,GAAG,EAAE,EAAE,GAAG,OAAO,CAAA;IAChC,MAAM,eAAe,GAAQ,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IACpD,IAAI,CAAC,eAAe,CAAC,MAAM,EAAE;QAC3B,OAAO,IAAI,CAAA;KACZ;IACD,MAAM,UAAU,GAAG,CAAC,QAAQ,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CACtE,KAAK,CAAC,EAAE,CAAC,CAAC;QACR,KAAK;KACN,CAAC,CACH,CAAA;IACD,IAAI,KAAK,CAAA;IACT,IAAI,IAAI,GAAG,EAAE,CAAA;IACb,MAAM,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IAEnC,qCAAqC;IACrC,wEAAwE;IACxE,4BAA4B;IAC5B,IAAI;QACF,IAAI,GAAG,eAAe;aACnB,GAAG,CAAC,CAAC,GAAQ,EAAE,EAAE,CAAC,CAAC;YAClB,GAAG,MAAM,CAAC,WAAW,CACnB,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAClE;YACD,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC;YACd,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;SACX,CAAC,CAAC;aACF,MAAM,CAAC,CAAC,GAAQ,EAAE,EAAE;YACnB,OAAO,OAAO,CAAC,MAAM;gBACnB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;oBAClB,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;oBACpB,MAAM,UAAU,GAAG,MAAM,CAAC,GAAG,CAAC,CAAA;oBAC9B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,MAAM,CAAC,UAAU,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;gBACnE,CAAC,CAAC;gBACJ,CAAC,CAAC,IAAI,CAAA;QACV,CAAC,CAAC,CAAA;KACL;IAAC,OAAO,CAAC,EAAE;QACV,KAAK,GAAG,CAAC,CAAA;KACV;IACD,sCAAsC;IACtC,uDAAuD;IACvD,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,SAAS;QACjC,KAAK,CAAC,CAAC,CAAC,8BAAC,qBAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI;QAEnE,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,WAAW,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,GACvC,EAEJ,KAAK,EAAC,qBAAqB,GAC3B;QACD,WAAW,CAAC,CAAC,CAAC,CACb;YACE,8BAAC,qBAAU,yQAKE;YACZ,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE;gBAC5B,OAAO,CACL,8BAAC,oBAAS,IACR,GAAG,EAAE,UAAU,KAAK,EAAE,EACtB,WAAW,EAAE,UAAU,KAAK,EAAE,EAC9B,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,EAAE,EAC1B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAChB,SAAS,CAAC,EAAE,GAAG,MAAM,EAAE,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,GAEvD,CACH,CAAA;YACH,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QACR,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;YAC1D,8BAAC,sBAAQ,IACP,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,UAAU,EACnB,uBAAuB,QACvB,SAAS,EAAE,EAAE,EACb,iBAAiB,SACjB,CACE,CACG,CACZ,CAAA;AACH,CAAC;AA3FD,iCA2FC"}

package/dist/VariantFeatureWidget/index.d.ts

@@ -35,3 +35,5 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/VariantFeatureWidget/index.js

@@ -1,16 +1,53 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = exports.configSchema = void 0;
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const react_1 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 exports.configSchema = (0, configuration_1.ConfigurationSchema)('VariantFeatureWidget', {});
 function stateModelFactory(pluginManager) {
-    var baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
+    const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
     return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('VariantFeatureWidget', {
         type: mobx_state_tree_1.types.literal('VariantFeatureWidget'),
         descriptions: mobx_state_tree_1.types.frozen(),
     }));
 }
 exports.stateModelFactory = stateModelFactory;
+exports.default = (pluginManager) => {
+    pluginManager.addWidgetType(() => new WidgetType_1.default({
+        name: 'VariantFeatureWidget',
+        heading: 'Feature details',
+        configSchema: exports.configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/VariantFeatureWidget/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/index.ts"],"names":[],"mappings":";;;AAAA,6DAAiE;AAEjE,mDAAuC;AACvC,qEAAuF;AAE1E,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAE3E,SAAgB,iBAAiB,CAAC,aAA4B;IAC5D,IAAM,SAAS,GAAG,IAAA,qCAAgB,EAAC,aAAa,CAAC,CAAA;IACjD,OAAO,uBAAK,CAAC,OAAO,CAClB,SAAS,EACT,uBAAK,CAAC,KAAK,CAAC,sBAAsB,EAAE;QAClC,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,YAAY,EAAE,uBAAK,CAAC,MAAM,EAAE;KAC7B,CAAC,CACH,CAAA;AACH,CAAC;AATD,8CASC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAC5B,+DAAiE;AACjE,gGAAuE;AAEvE,qDAAuC;AACvC,uEAAuF;AAE1E,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAE3E,SAAgB,iBAAiB,CAAC,aAA4B;IAC5D,MAAM,SAAS,GAAG,IAAA,qCAAgB,EAAC,aAAa,CAAC,CAAA;IACjD,OAAO,uBAAK,CAAC,OAAO,CAClB,SAAS,EACT,uBAAK,CAAC,KAAK,CAAC,sBAAsB,EAAE;QAClC,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,YAAY,EAAE,uBAAK,CAAC,MAAM,EAAE;KAC7B,CAAC,CACH,CAAA;AACH,CAAC;AATD,8CASC;AAED,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,aAAa,CACzB,GAAG,EAAE,CACH,IAAI,oBAAU,CAAC;QACb,IAAI,EAAE,sBAAsB;QAC5B,OAAO,EAAE,iBAAiB;QAC1B,YAAY,EAAZ,oBAAY;QACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,CAAC;QAC5C,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,wBAAwB,GAAC,CAAC;KAC7D,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/VariantTrack/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/VariantTrack/index.js

@@ -0,0 +1,19 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+exports.default = (pluginManager) => {
+    pluginManager.addTrackType(() => {
+        const configSchema = (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
+        return new TrackType_1.default({
+            name: 'VariantTrack',
+            configSchema,
+            stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'VariantTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/VariantTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":";;;;;AACA,+DAAiE;AACjE,8FAAqE;AACrE,uEAGmD;AAEnD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,cAAc,EACd,EAAE,EACF,EAAE,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;QACD,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,cAAc,EACd,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/VcfAdapter/VcfAdapter.js

@@ -1,88 +1,22 @@
 "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 });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var configuration_1 = require("@jbrowse/core/configuration");
-var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-var vcf_1 = __importDefault(require("@gmod/vcf"));
-var VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
-var readVcf = function (f) {
-    var lines = f.split('\n');
-    var header = [];
-    var rest = [];
-    lines.forEach(function (line) {
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const vcf_1 = __importDefault(require("@gmod/vcf"));
+const VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
+const readVcf = (f) => {
+    const header = [];
+    const rest = [];
+    f.split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f)
+        .forEach(line => {
         if (line.startsWith('#')) {
             header.push(line);
         }
@@ -95,149 +29,79 @@ var readVcf = function (f) {
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-var VcfAdapter = /** @class */ (function (_super) {
-    __extends(VcfAdapter, _super);
-    function VcfAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
+class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    async getHeader() {
+        const { header } = await this.setup();
+        return header;
+    }
+    async getMetadata() {
+        const { header } = await this.setup();
+        const parser = new vcf_1.default({ header: header });
+        return parser.getMetadata();
     }
-    VcfAdapter.prototype.getHeader = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var header;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup()];
-                    case 1:
-                        header = (_a.sent()).header;
-                        return [2 /*return*/, header];
-                }
-            });
-        });
-    };
-    VcfAdapter.prototype.getMetadata = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var header, parser;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup()];
-                    case 1:
-                        header = (_a.sent()).header;
-                        parser = new vcf_1.default({ header: header });
-                        return [2 /*return*/, parser.getMetadata()];
-                }
-            });
-        });
-    };
     // converts lines into an interval tree
-    VcfAdapter.prototype.setupP = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var buffer, buf, _a, str, _b, header, lines, intervalTree;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0: return [4 /*yield*/, (0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'vcfLocation'), this.pluginManager).readFile()];
-                    case 1:
-                        buffer = _c.sent();
-                        if (!isGzip(buffer)) return [3 /*break*/, 3];
-                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)];
-                    case 2:
-                        _a = _c.sent();
-                        return [3 /*break*/, 4];
-                    case 3:
-                        _a = buffer;
-                        _c.label = 4;
-                    case 4:
-                        buf = _a;
-                        // 512MB  max chrome string length is 512MB
-                        if (buf.length > 536870888) {
-                            throw new Error('Data exceeds maximum string length (512MB)');
-                        }
-                        str = new TextDecoder().decode(buf);
-                        _b = readVcf(str), header = _b.header, lines = _b.lines;
-                        intervalTree = lines
-                            .map(function (line, id) {
-                            var _a;
-                            var _b = __read(line.split('\t'), 8), refName = _b[0], startP = _b[1], ref = _b[3], info = _b[7];
-                            var start = +startP - 1;
-                            var end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
-                            return { line: line, refName: refName, start: start, end: end, id: id };
-                        })
-                            .reduce(function (acc, obj) {
-                            var key = obj.refName;
-                            if (!acc[key]) {
-                                acc[key] = new interval_tree_1.default();
-                            }
-                            acc[key].insert([obj.start, obj.end], obj);
-                            return acc;
-                        }, {});
-                        return [2 /*return*/, { header: header, intervalTree: intervalTree }];
-                }
-            });
-        });
-    };
-    VcfAdapter.prototype.setup = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.vcfFeatures) {
-                    this.vcfFeatures = this.setupP().catch(function (e) {
-                        _this.vcfFeatures = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.vcfFeatures];
-            });
-        });
-    };
-    VcfAdapter.prototype.getRefNames = function (_) {
-        if (_ === void 0) { _ = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var intervalTree;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup()];
-                    case 1:
-                        intervalTree = (_a.sent()).intervalTree;
-                        return [2 /*return*/, Object.keys(intervalTree)];
-                }
-            });
-        });
-    };
-    VcfAdapter.prototype.getFeatures = function (region, opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var start, end, refName, _a, header, intervalTree, parser_1, e_1;
-            var _this = this;
-            var _b;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        _c.trys.push([0, 2, , 3]);
-                        start = region.start, end = region.end, refName = region.refName;
-                        return [4 /*yield*/, this.setup()];
-                    case 1:
-                        _a = _c.sent(), header = _a.header, intervalTree = _a.intervalTree;
-                        parser_1 = new vcf_1.default({ header: header });
-                        (_b = intervalTree[refName]) === null || _b === void 0 ? void 0 : _b.search([start, end]).forEach(function (f) {
-                            return observer.next(new VcfFeature_1.default({
-                                variant: parser_1.parseLine(f.line),
-                                parser: parser_1,
-                                id: "".concat(_this.id, "-").concat(f.id),
-                            }));
-                        });
-                        observer.complete();
-                        return [3 /*break*/, 3];
-                    case 2:
-                        e_1 = _c.sent();
-                        observer.error(e_1);
-                        return [3 /*break*/, 3];
-                    case 3: return [2 /*return*/];
-                }
+    async setupP() {
+        const pm = this.pluginManager;
+        const buf = await (0, io_1.openLocation)(this.getConf('vcfLocation'), pm).readFile();
+        const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        // 512MB  max chrome string length is 512MB
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const str = new TextDecoder().decode(buffer);
+        const { header, lines } = readVcf(str);
+        const intervalTree = lines
+            .map((line, id) => {
+            var _a;
+            const [refName, startP, , ref, , , , info] = line.split('\t');
+            const start = +startP - 1;
+            const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
+            return { line, refName, start, end, id };
+        })
+            .reduce((acc, obj) => {
+            const key = obj.refName;
+            if (!acc[key]) {
+                acc[key] = new interval_tree_1.default();
+            }
+            acc[key].insert([obj.start, obj.end], obj);
+            return acc;
+        }, {});
+        return { header, intervalTree };
+    }
+    async setup() {
+        if (!this.vcfFeatures) {
+            this.vcfFeatures = this.setupP().catch(e => {
+                this.vcfFeatures = undefined;
+                throw e;
             });
-        }); }, opts.signal);
-    };
-    VcfAdapter.prototype.freeResources = function () { };
-    VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
-    return VcfAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+        }
+        return this.vcfFeatures;
+    }
+    async getRefNames(_ = {}) {
+        const { intervalTree } = await this.setup();
+        return Object.keys(intervalTree);
+    }
+    getFeatures(region, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            var _a;
+            try {
+                const { start, end, refName } = region;
+                const { header, intervalTree } = await this.setup();
+                const parser = new vcf_1.default({ header: header });
+                (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature_1.default({
+                    variant: parser.parseLine(f.line),
+                    parser,
+                    id: `${this.id}-${f.id}`,
+                })));
+                observer.complete();
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        }, opts.signal);
+    }
+    freeResources() { }
+}
 exports.default = VcfAdapter;
+VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
 //# sourceMappingURL=VcfAdapter.js.map

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAEhD,4CAAoD;AACpD,gDAA0D;AAE1D,6DAA4D;AAC5D,4EAAoD;AACpD,yDAA6C;AAC7C,kDAA2B;AAC3B,6EAAsD;AAEtD,IAAM,OAAO,GAAG,UAAC,CAAS;IACxB,IAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,IAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,IAAM,IAAI,GAAa,EAAE,CAAA;IACzB,KAAK,CAAC,OAAO,CAAC,UAAA,IAAI;QAChB,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACF,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED;IAAwC,8BAAsB;IAA9D;;IA6FA,CAAC;IArFc,8BAAS,GAAtB;;;;;4BACqB,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA7B,MAAM,GAAK,CAAA,SAAkB,CAAA,OAAvB;wBACd,sBAAO,MAAM,EAAA;;;;KACd;IAEK,gCAAW,GAAjB;;;;;4BACqB,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA7B,MAAM,GAAK,CAAA,SAAkB,CAAA,OAAvB;wBACR,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;wBAC1C,sBAAO,MAAM,CAAC,WAAW,EAAE,EAAA;;;;KAC5B;IAED,uCAAuC;IAC1B,2BAAM,GAAnB;;;;;4BACiB,qBAAM,IAAA,iBAAY,EAC/B,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,aAAa,CAAC,EAC1C,IAAI,CAAC,aAAa,CACnB,CAAC,QAAQ,EAAE,EAAA;;wBAHN,MAAM,GAAG,SAGH;6BAEA,MAAM,CAAC,MAAM,CAAC,EAAd,wBAAc;wBAAG,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,EAAA;;wBAAnB,KAAA,SAAmB,CAAA;;;wBAAG,KAAA,MAAM,CAAA;;;wBAAnD,GAAG,KAAgD;wBAEzD,2CAA2C;wBAC3C,IAAI,GAAG,CAAC,MAAM,GAAG,SAAW,EAAE;4BAC5B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;yBAC9D;wBAEK,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;wBACnC,KAAoB,OAAO,CAAC,GAAG,CAAC,EAA9B,MAAM,YAAA,EAAE,KAAK,WAAA,CAAiB;wBAEhC,YAAY,GAAG,KAAK;6BACvB,GAAG,CAAC,UAAC,IAAI,EAAE,EAAE;;4BACN,IAAA,KAAA,OAAuC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAA,EAAtD,OAAO,QAAA,EAAE,MAAM,QAAA,EAAI,GAAG,QAAA,EAAQ,IAAI,QAAoB,CAAA;4BAC7D,IAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;4BACzB,IAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;4BACxE,OAAO,EAAE,IAAI,MAAA,EAAE,OAAO,SAAA,EAAE,KAAK,OAAA,EAAE,GAAG,KAAA,EAAE,EAAE,IAAA,EAAE,CAAA;wBAC1C,CAAC,CAAC;6BACD,MAAM,CAAC,UAAC,GAAG,EAAE,GAAG;4BACf,IAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;4BACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gCACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;6BAC9B;4BACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;4BAC1C,OAAO,GAAG,CAAA;wBACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;wBAExC,sBAAO,EAAE,MAAM,QAAA,EAAE,YAAY,cAAA,EAAE,EAAA;;;;KAChC;IAEY,0BAAK,GAAlB;;;;gBACE,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;oBACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,UAAA,CAAC;wBACtC,KAAI,CAAC,WAAW,GAAG,SAAS,CAAA;wBAC5B,MAAM,CAAC,CAAA;oBACT,CAAC,CAAC,CAAA;iBACH;gBACD,sBAAO,IAAI,CAAC,WAAW,EAAA;;;KACxB;IAEY,gCAAW,GAAxB,UAAyB,CAAmB;QAAnB,kBAAA,EAAA,MAAmB;;;;;4BACjB,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAAnC,YAAY,GAAK,CAAA,SAAkB,CAAA,aAAvB;wBACpB,sBAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,EAAA;;;;KACjC;IAEM,gCAAW,GAAlB,UAAmB,MAAc,EAAE,IAAsB;QAAzD,iBAoBC;QApBkC,qBAAA,EAAA,SAAsB;QACvD,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;;;;;;wBAEnC,KAAK,GAAmB,MAAM,MAAzB,EAAE,GAAG,GAAc,MAAM,IAApB,EAAE,OAAO,GAAK,MAAM,QAAX,CAAW;wBACL,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA7C,KAA2B,SAAkB,EAA3C,MAAM,YAAA,EAAE,YAAY,kBAAA;wBACtB,WAAS,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;wBAC1C,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,UAAA,CAAC;4BACnD,OAAA,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;gCACb,OAAO,EAAE,QAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;gCACjC,MAAM,UAAA;gCACN,EAAE,EAAE,UAAG,KAAI,CAAC,EAAE,cAAI,CAAC,CAAC,EAAE,CAAE;6BACzB,CAAC,CACH;wBAND,CAMC,CACF,CAAA;wBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;;wBAEnB,QAAQ,CAAC,KAAK,CAAC,GAAC,CAAC,CAAA;;;;;aAEpB,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,kCAAa,GAApB,cAA8B,CAAC;IA3FjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;IA4F7D,iBAAC;CAAA,AA7FD,CAAwC,oCAAsB,GA6F7D;kBA7FoB,UAAU"}
+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAE1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAC3B,+EAAsD;AAEtD,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;gBAC1C,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;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;;AA1FjC,6BA2FC;AA1Fe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}

package/dist/VcfAdapter/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)('VcfAdapter', {
     vcfLocation: {
         type: 'fileLocation',

package/dist/VcfAdapter/configSchema.js.map

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

package/dist/VcfAdapter/index.d.ts

@@ -1 +1,3 @@
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/VcfAdapter/index.js

@@ -1,9 +1,38 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'VcfAdapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/VcfAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}