@jbrowse/plugin-variants 2.0.0 → 2.1.2

package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAMhD,8CAAoD;AACpD,6CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,oDAAiC;AAEjC,+DAA4D;AAC5D,8DAAqC;AAGrC,eAAqB,SAAQ,oCAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAClE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACnE,MAAM,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAErE,MAAM,UAAU,GAAG,IAAA,iBAAY,EAC7B,aAA6B,EAC7B,IAAI,CAAC,aAAa,CACnB,CAAA;QACD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK;gBAClB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,aAAa,EAAE,CAAC,KAAK;gBACnB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,UAAU;YACV,GAAG;YACH,MAAM,EAAE,IAAI,aAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;oBACjD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,4BAA4B,CACjC,OAAiB,EACjB,OAAoB,EAAE;QAEtB,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,CAAA;YACvD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,IAAI,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACpC,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;YAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;gBACb,yDAAyD;gBACzD,GAAG,GAAG,GAAG,CAAA;aACV;YACD,IAAI,GAAG,GAAG,EAAE,EAAE;gBACZ,OAAO,CAAC,IAAI,CACV,yCAAyC,GAAG,6DAA6D,CAC1G,CAAA;aACF;YACD,KAAK,CAAC,4BAA4B,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACvE,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA1HD,4BA0HC"}

package/dist/VcfTabixAdapter/configSchema.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var mobx_state_tree_1 = require("mobx-state-tree");
-var configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.default = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
     vcfGzLocation: {
         type: 'fileLocation',

package/dist/VcfTabixAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,mDAAuC;AACvC,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,IAAA,mCAAmB,EAAC,UAAU,EAAE;QACrC,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;CACH,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,IAAA,mCAAmB,EAAC,UAAU,EAAE;QACrC,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;CACH,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/VcfTabixAdapter/index.d.ts

@@ -1 +1,4 @@
+import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/VcfTabixAdapter/index.js

@@ -1,9 +1,41 @@
 "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"));
+var configSchema_2 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'VcfTabixAdapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/VcfTabixAdapter/index.js.map

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

package/dist/extensionPoints.d.ts

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

package/dist/extensionPoints.js

@@ -0,0 +1,51 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tracks_1 = require("@jbrowse/core/util/tracks");
+exports.default = (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.vcf\.b?gz$/i;
+            const adapterName = 'VcfTabixAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const indexName = index && (0, tracks_1.getFileName)(index);
+            const obj = {
+                type: adapterName,
+                vcfGzLocation: file,
+                index: {
+                    location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                },
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
+                return 'VariantTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.vcf$/i;
+            const adapterName = 'VcfAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                return {
+                    type: adapterName,
+                    vcfLocation: file,
+                };
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+};
+//# sourceMappingURL=extensionPoints.js.map

package/dist/extensionPoints.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"extensionPoints.js","sourceRoot":"","sources":["../src/extensionPoints.ts"],"names":[],"mappings":";;AAEA,sDAMkC;AAElC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,eAAe,CAAA;YAClC,MAAM,WAAW,GAAG,iBAAiB,CAAA;YACrC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;YAC7C,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,aAAa,EAAE,IAAI;gBACnB,KAAK,EAAE;oBACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;oBAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;iBAClD;aACF,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;QACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;YAC7B,IAAI,WAAW,KAAK,iBAAiB,IAAI,WAAW,KAAK,YAAY,EAAE;gBACrE,OAAO,cAAc,CAAA;aACtB;YACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;QACtC,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,SAAS,CAAA;YAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;YAChC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;gBAC5D,OAAO;oBACL,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;iBAClB,CAAA;aACF;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}

package/dist/index.js

@@ -1,172 +1,34 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    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.VcfFeature = void 0;
-var react_1 = require("react");
-var configuration_1 = require("@jbrowse/core/configuration");
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-var WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-var ChordVariantDisplay_1 = __importDefault(require("./ChordVariantDisplay"));
-var LinearVariantDisplay_1 = require("./LinearVariantDisplay");
-var StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
-var VariantFeatureWidget_1 = require("./VariantFeatureWidget");
-var VcfTabixAdapter_1 = require("./VcfTabixAdapter");
-var VcfAdapter_1 = require("./VcfAdapter");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var VariantsPlugin = /** @class */ (function (_super) {
-    __extends(VariantsPlugin, _super);
-    function VariantsPlugin() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'VariantsPlugin';
-        return _this;
+const VcfAdapter_1 = __importDefault(require("./VcfAdapter"));
+const VcfTabixAdapter_1 = __importDefault(require("./VcfTabixAdapter"));
+const extensionPoints_1 = __importDefault(require("./extensionPoints"));
+const VariantTrack_1 = __importDefault(require("./VariantTrack"));
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const ChordVariantDisplay_1 = __importDefault(require("./ChordVariantDisplay"));
+const LinearVariantDisplay_1 = __importDefault(require("./LinearVariantDisplay"));
+const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
+const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
+class VariantsPlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'VariantsPlugin';
+    }
+    install(pluginManager) {
+        (0, VcfAdapter_1.default)(pluginManager);
+        (0, VcfTabixAdapter_1.default)(pluginManager);
+        (0, VariantFeatureWidget_1.default)(pluginManager);
+        (0, VariantTrack_1.default)(pluginManager);
+        (0, extensionPoints_1.default)(pluginManager);
+        (0, LinearVariantDisplay_1.default)(pluginManager);
+        pluginManager.addRendererType(() => pluginManager.jbrequire(StructuralVariantChordRenderer_1.default));
+        pluginManager.addDisplayType(() => pluginManager.jbrequire(ChordVariantDisplay_1.default));
     }
-    VariantsPlugin.prototype.install = function (pluginManager) {
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'VcfTabixAdapter',
-                configSchema: VcfTabixAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./VcfTabixAdapter/VcfTabixAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.vcf\.b?gz$/i;
-                var adapterName = 'VcfTabixAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var indexName = index && (0, tracks_1.getFileName)(index);
-                var obj = {
-                    type: adapterName,
-                    vcfGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-            return function (adapterName) {
-                if (adapterName === 'VcfTabixAdapter' ||
-                    adapterName === 'VcfAdapter') {
-                    return 'VariantTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'VcfAdapter',
-                configSchema: VcfAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./VcfAdapter/VcfAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.vcf$/i;
-                var adapterName = 'VcfAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        vcfLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addRendererType(function () {
-            return pluginManager.jbrequire(StructuralVariantChordRenderer_1.default);
-        });
-        pluginManager.addTrackType(function () {
-            var configSchema = (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
-            return new TrackType_1.default({
-                name: 'VariantTrack',
-                configSchema: configSchema,
-                stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'VariantTrack', configSchema),
-            });
-        });
-        pluginManager.addDisplayType(function () {
-            return pluginManager.jbrequire(ChordVariantDisplay_1.default);
-        });
-        pluginManager.addDisplayType(function () {
-            var configSchema = (0, LinearVariantDisplay_1.configSchemaFactory)(pluginManager);
-            return new DisplayType_1.default({
-                name: 'LinearVariantDisplay',
-                configSchema: configSchema,
-                stateModel: (0, LinearVariantDisplay_1.modelFactory)(configSchema),
-                trackType: 'VariantTrack',
-                viewType: 'LinearGenomeView',
-                ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
-            });
-        });
-        pluginManager.addWidgetType(function () {
-            return new WidgetType_1.default({
-                name: 'VariantFeatureWidget',
-                heading: 'Feature details',
-                configSchema: VariantFeatureWidget_1.configSchema,
-                stateModel: (0, VariantFeatureWidget_1.stateModelFactory)(pluginManager),
-                ReactComponent: (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./VariantFeatureWidget/VariantFeatureWidget')); }); }),
-            });
-        });
-    };
-    return VariantsPlugin;
-}(Plugin_1.default));
+}
 exports.default = VariantsPlugin;
 var VcfFeature_1 = require("./VcfTabixAdapter/VcfFeature");
 Object.defineProperty(exports, "VcfFeature", { enumerable: true, get: function () { return __importDefault(VcfFeature_1).default; } });

package/dist/index.js.map

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package/esm/LinearVariantDisplay/index.d.ts

@@ -1,2 +1,3 @@
-export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
-export { default as modelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinearVariantDisplay/index.js

@@ -1,3 +1,18 @@
-export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
-export { default as modelFactory } from './model';
+import { LinearVariantDisplayConfigFactory } from './configSchema';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import stateModelFactory from './model';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = LinearVariantDisplayConfigFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearVariantDisplay',
+            configSchema,
+            stateModel: stateModelFactory(configSchema),
+            trackType: 'VariantTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
 //# sourceMappingURL=index.js.map

package/esm/LinearVariantDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iCAAiC,EAAE,MAAM,gBAAgB,CAAA;AAClE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAC/E,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,iBAAiB,MAAM,SAAS,CAAA;AAEvC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,iCAAiC,CAAC,aAAa,CAAC,CAAA;QACrE,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/VariantFeatureWidget/AnnotGrid.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantAnnotPanel({ rows, columns, }: {
+    rows: any;
+    columns: any[];
+}): JSX.Element | null;

package/esm/VariantFeatureWidget/AnnotGrid.js

@@ -0,0 +1,16 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { DataGrid } from '@mui/x-data-grid';
+export default function VariantAnnotPanel({ rows, columns, }) {
+    const rowHeight = 25;
+    const hideFooter = rows.length < 100;
+    const headerHeight = 80;
+    return rows.length ? (React.createElement("div", { style: {
+            height: Math.min(rows.length, 100) * rowHeight +
+                headerHeight +
+                (hideFooter ? 0 : 50),
+            width: '100%',
+        } },
+        React.createElement(DataGrid, { rowHeight: rowHeight, rows: rows, columns: columns }))) : null;
+}
+//# sourceMappingURL=AnnotGrid.js.map

package/esm/VariantFeatureWidget/AnnotGrid.js.map

@@ -0,0 +1 @@
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package/esm/VariantFeatureWidget/BreakendPanel.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+export default function BreakendPanel(props: {
+    locStrings: string[];
+    model: any;
+    feature: SimpleFeatureSerialized;
+}): JSX.Element;

package/esm/VariantFeatureWidget/BreakendPanel.js

@@ -0,0 +1,53 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React, { useState } from 'react';
+import { Link, Typography } from '@mui/material';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { getSession } from '@jbrowse/core/util';
+import { getEnv } from 'mobx-state-tree';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import BreakendOptionDialog from './BreakendOptionDialog';
+export default function BreakendPanel(props) {
+    const { model, locStrings, feature } = props;
+    const session = getSession(model);
+    const { pluginManager } = getEnv(session);
+    const [breakpointDialog, setBreakpointDialog] = useState(false);
+    let viewType;
+    try {
+        viewType = pluginManager.getViewType('BreakpointSplitView');
+    }
+    catch (e) {
+        // ignore
+    }
+    const simpleFeature = new SimpleFeature(feature);
+    return (React.createElement(BaseCard, { ...props, title: "Breakends" },
+        React.createElement(Typography, null, "Link to linear view of breakend endpoints"),
+        React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
+            React.createElement(Link, { href: "#", onClick: event => {
+                    var _a;
+                    event.preventDefault();
+                    const { view } = model;
+                    try {
+                        if (view) {
+                            (_a = view.navToLocString) === null || _a === void 0 ? void 0 : _a.call(view, locString);
+                        }
+                        else {
+                            throw new Error('No view associated with this feature detail panel anymore');
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                } }, `LGV - ${locString}`))))),
+        viewType ? (React.createElement("div", null,
+            React.createElement(Typography, null, "Launch split views with breakend source and target"),
+            React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
+                React.createElement(Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        setBreakpointDialog(true);
+                    } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
+            breakpointDialog ? (React.createElement(BreakendOptionDialog, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
+                    setBreakpointDialog(false);
+                } })) : null)) : null));
+}
+//# sourceMappingURL=BreakendPanel.js.map

package/esm/VariantFeatureWidget/BreakendPanel.js.map

@@ -0,0 +1 @@
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package/esm/VariantFeatureWidget/VariantAnnPanel.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantAnnPanel({ feature, descriptions, }: {
+    feature: any;
+    descriptions: any;
+}): JSX.Element | null;

package/esm/VariantFeatureWidget/VariantAnnPanel.js

@@ -0,0 +1,19 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import AnnotGrid from './AnnotGrid';
+export default function VariantAnnPanel({ feature, descriptions, }) {
+    var _a, _b, _c, _d;
+    const annFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Functional annotations:'(.*)'$/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
+    const ann = (feature.INFO.ANN || []);
+    const rows = ann.map((elt, id) => ({
+        id,
+        ...Object.fromEntries(elt.split('|').map((e, i) => [annFields[i], e])),
+    })) || [];
+    const columns = annFields.map(c => ({
+        field: c,
+    }));
+    return ann.length ? (React.createElement(BaseCard, { title: "ANN table" },
+        React.createElement(AnnotGrid, { rows: rows, columns: columns }))) : null;
+}
+//# sourceMappingURL=VariantAnnPanel.js.map

package/esm/VariantFeatureWidget/VariantAnnPanel.js.map

@@ -0,0 +1 @@
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package/esm/VariantFeatureWidget/VariantCsqPanel.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function VariantCsqPanel({ feature, descriptions, }: {
+    feature: any;
+    descriptions: any;
+}): JSX.Element | null;

package/esm/VariantFeatureWidget/VariantCsqPanel.js

@@ -0,0 +1,19 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import AnnotGrid from './AnnotGrid';
+export default function VariantCsqPanel({ feature, descriptions, }) {
+    var _a, _b, _c, _d;
+    const csqFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Format: (.*)/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
+    const csq = (feature.INFO.CSQ || []);
+    const rows = csq.map((elt, id) => ({
+        id,
+        ...Object.fromEntries(elt.split('|').map((e, i) => [csqFields[i], e])),
+    })) || [];
+    const columns = csqFields.map(c => ({
+        field: c,
+    }));
+    return csq.length ? (React.createElement(BaseCard, { title: "CSQ table" },
+        React.createElement(AnnotGrid, { rows: rows, columns: columns }))) : null;
+}
+//# sourceMappingURL=VariantCsqPanel.js.map

package/esm/VariantFeatureWidget/VariantCsqPanel.js.map

@@ -0,0 +1 @@
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