npm - @jbrowse/plugin-trix - Versions diffs - 2.0.0 → 2.1.2 - Mend

@jbrowse/plugin-trix 2.0.0 → 2.1.2

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Files changed (12) hide show

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js +47 -136
package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map +1 -1
package/dist/TrixTextSearchAdapter/configSchema.js +1 -1
package/dist/TrixTextSearchAdapter/configSchema.js.map +1 -1
package/dist/index.js +16 -36
package/dist/index.js.map +1 -1
package/package.json +4 -5
package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts +7 -12
package/src/TrixTextSearchAdapter/test_data/volvox.ix +194 -0
package/src/TrixTextSearchAdapter/test_data/volvox.ixx +1 -0
package/src/TrixTextSearchAdapter/test_data/volvox2_meta.json +1 -0
package/src/TrixTextSearchAdapter/test_data/volvox_meta.json +163 -0

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js CHANGED Viewed

@@ -1,80 +1,13 @@
 "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 trix_1 = __importDefault(require("@gmod/trix"));
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-var configuration_1 = require("@jbrowse/core/configuration");
+const trix_1 = __importDefault(require("@gmod/trix"));
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+const configuration_1 = require("@jbrowse/core/configuration");
 function decodeURIComponentNoThrow(uri) {
     try {
         return decodeURIComponent(uri);
@@ -84,89 +17,67 @@ function decodeURIComponentNoThrow(uri) {
         return uri;
     }
 }
-function shorten(str, term, w) {
-    if (w === void 0) { w = 15; }
-    var tidx = str.toLowerCase().indexOf(term);
+function shorten(str, term, w = 15) {
+    const tidx = str.toLowerCase().indexOf(term);
     return str.length < 40
         ? str
         : (Math.max(0, tidx - w) > 0 ? '...' : '') +
             str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +
             (tidx + term.length < str.length ? '...' : '');
 }
-var TrixTextSearchAdapter = /** @class */ (function (_super) {
-    __extends(TrixTextSearchAdapter, _super);
-    function TrixTextSearchAdapter(config, getSubAdapter, pluginManager) {
-        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
-        var ixFilePath = (0, configuration_1.readConfObject)(config, 'ixFilePath');
-        var ixxFilePath = (0, configuration_1.readConfObject)(config, 'ixxFilePath');
+class TrixTextSearchAdapter extends BaseAdapter_1.BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const ixFilePath = (0, configuration_1.readConfObject)(config, 'ixFilePath');
+        const ixxFilePath = (0, configuration_1.readConfObject)(config, 'ixxFilePath');
         if (!ixFilePath) {
             throw new Error('must provide out.ix');
         }
         if (!ixxFilePath) {
             throw new Error('must provide out.ixx');
         }
-        _this.trixJs = new trix_1.default((0, io_1.openLocation)(ixxFilePath), (0, io_1.openLocation)(ixFilePath), 1500);
-        return _this;
+        this.trixJs = new trix_1.default((0, io_1.openLocation)(ixxFilePath), (0, io_1.openLocation)(ixFilePath), 1500);
     }
     /*
      * Returns list of results
      * @param args - search options/arguments include: search query
      * limit of results to return, searchType...prefix | full | exact", etc.
      */
-    TrixTextSearchAdapter.prototype.searchIndex = function (args) {
-        return __awaiter(this, void 0, void 0, function () {
-            var query, strs, results, formatted;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        query = args.queryString.toLowerCase();
-                        strs = query.split(' ');
-                        return [4 /*yield*/, this.trixJs.search(query)];
-                    case 1:
-                        results = _a.sent();
-                        formatted = results
-                            // if multi-word search try to filter out relevant items
-                            .filter(function (_a) {
-                            var _b = __read(_a, 2), data = _b[1];
-                            return strs.every(function (r) {
-                                return decodeURIComponentNoThrow(data).toLowerCase().includes(r);
-                            });
-                        })
-                            .map(function (_a) {
-                            var _b = __read(_a, 2), term = _b[0], data = _b[1];
-                            var result = JSON.parse(data.replace(/\|/g, ','));
-                            var _c = __read(result.map(function (record) {
-                                return decodeURIComponentNoThrow(record);
-                            })), loc = _c[0], trackId = _c[1], rest = _c.slice(2);
-                            var labelFieldIdx = rest.findIndex(function (elt) { return !!elt; });
-                            var contextIdx = rest
-                                .map(function (elt) { return elt.toLowerCase(); })
-                                .findIndex(function (f) { return f.indexOf(term.toLowerCase()) !== -1; });
-                            var labelField = rest[labelFieldIdx];
-                            var contextField = rest[contextIdx];
-                            var context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
-                            var label = shorten(labelField, term);
-                            var displayString = !context || label.toLowerCase() === context.toLowerCase()
-                                ? label
-                                : "".concat(label, " (").concat(context, ")");
-                            return new BaseResults_1.default({
-                                locString: loc,
-                                label: labelField,
-                                displayString: displayString,
-                                matchedObject: result.map(function (record) { return decodeURIComponent(record); }),
-                                trackId: trackId,
-                            });
-                        });
-                        if (args.searchType === 'exact') {
-                            return [2 /*return*/, formatted.filter(function (res) { return res.getLabel().toLowerCase() === args.queryString.toLowerCase(); })];
-                        }
-                        return [2 /*return*/, formatted];
-                }
+    async searchIndex(args) {
+        const query = args.queryString.toLowerCase();
+        const strs = query.split(' ');
+        const results = await this.trixJs.search(query);
+        const formatted = results
+            // if multi-word search try to filter out relevant items
+            .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
+            .map(([term, data]) => {
+            const result = JSON.parse(data.replace(/\|/g, ','));
+            const [loc, trackId, ...rest] = result.map(record => decodeURIComponentNoThrow(record));
+            const labelFieldIdx = rest.findIndex(elt => !!elt);
+            const contextIdx = rest
+                .map(elt => elt.toLowerCase())
+                .findIndex(f => f.indexOf(term.toLowerCase()) !== -1);
+            const labelField = rest[labelFieldIdx];
+            const contextField = rest[contextIdx];
+            const context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
+            const label = shorten(labelField, term);
+            const displayString = !context || label.toLowerCase() === context.toLowerCase()
+                ? label
+                : `${label} (${context})`;
+            return new BaseResults_1.default({
+                locString: loc,
+                label: labelField,
+                displayString,
+                matchedObject: result.map(record => decodeURIComponent(record)),
+                trackId,
             });
         });
-    };
-    TrixTextSearchAdapter.prototype.freeResources = function () { };
-    return TrixTextSearchAdapter;
-}(BaseAdapter_1.BaseAdapter));
+        if (args.searchType === 'exact') {
+            return formatted.filter(res => res.getLabel().toLowerCase() === args.queryString.toLowerCase());
+        }
+        return formatted;
+    }
+    freeResources() { }
+}
 exports.default = TrixTextSearchAdapter;
 //# sourceMappingURL=TrixTextSearchAdapter.js.map

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map CHANGED Viewed

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package/dist/TrixTextSearchAdapter/configSchema.js CHANGED Viewed

@@ -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)('TrixTextSearchAdapter', {
     ixFilePath: {
         type: 'fileLocation',

package/dist/TrixTextSearchAdapter/configSchema.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.js CHANGED Viewed

@@ -1,44 +1,24 @@
 "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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var TrixTextSearchAdapter_1 = require("./TrixTextSearchAdapter");
-var default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'TrixPlugin';
-        return _this;
+const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const TrixTextSearchAdapter_1 = require("./TrixTextSearchAdapter");
+class default_1 extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'TrixPlugin';
     }
-    default_1.prototype.install = function (pluginManager) {
-        pluginManager.addTextSearchAdapterType(function () {
-            return new TextSearchAdapterType_1.default({
-                name: 'TrixTextSearchAdapter',
-                configSchema: TrixTextSearchAdapter_1.configSchema,
-                AdapterClass: TrixTextSearchAdapter_1.AdapterClass,
-                description: 'Trix adapter',
-            });
-        });
-    };
-    return default_1;
-}(Plugin_1.default));
+    install(pluginManager) {
+        pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType_1.default({
+            name: 'TrixTextSearchAdapter',
+            configSchema: TrixTextSearchAdapter_1.configSchema,
+            AdapterClass: TrixTextSearchAdapter_1.AdapterClass,
+            description: 'Trix adapter',
+        }));
+    }
+}
 exports.default = default_1;
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "2.0.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",
@@ -37,8 +37,8 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@mui/material": "^4.9.13",
+    "@jbrowse/core": "^2.0.0",
+    "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -46,7 +46,6 @@
     "react": ">=16.8.0"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@gmod/trix": "^2.0.4"
   },
   "publishConfig": {
@@ -55,5 +54,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts CHANGED Viewed

@@ -1,28 +1,23 @@
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import path from 'path'
 import Adapter from './TrixTextSearchAdapter'
+import path from 'path'
 import configSchema from './configSchema'
 test('adapter can fetch output files', async () => {
-  const rootTemplate = path
-    .join(__dirname, '..', '..', '..', '..', 'test_data', 'volvox', 'trix')
-    .replace(/\\/g, '\\\\')
-  const urlPath = decodeURI(new URL(`file://${rootTemplate}`).href)
   const args = {
     type: 'TrixTextSearchAdapter',
     textSearchAdapterId: 'TrixTextSearchAdapterTest',
     ixFilePath: {
-      uri: `${urlPath}/volvox.ix`,
-      locationType: 'UriLocation',
+      localPath: path.resolve(__dirname, `test_data/volvox.ix`),
+      locationType: 'LocalPathLocation',
     },
     ixxFilePath: {
-      uri: `${urlPath}/volvox.ixx`,
-      locationType: 'UriLocation',
+      localPath: path.resolve(__dirname, `test_data/volvox.ixx`),
+      locationType: 'LocalPathLocation',
     },
     metaFilePath: {
-      uri: `${urlPath}/volvox_meta.json`,
-      locationType: 'UriLocation',
+      localPath: path.resolve(__dirname, `test_data/volvox_meta.json`),
+      locationType: 'LocalPathLocation',
     },
   }
   // create adapter

package/src/TrixTextSearchAdapter/test_data/volvox.ix ADDED Viewed

@@ -0,0 +1,194 @@
+1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2
+1000 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
+3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
+7-transmembrane ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],2 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],3
+a ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+agt221.3 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
+agt221.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt221.5"],1 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt221.5"],3 ["ctgA%3A7000..7300"|"gff3tabix_genes"|"agt221.5"],4
+agt767.3 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
+agt767.5 ["ctgA%3A1150..1500"|"gff3tabix_genes"|"agt767.5"],1 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt767.5"],3 ["ctgA%3A7000..7200"|"gff3tabix_genes"|"agt767.5"],4
+agt830.3 ["ctgA%3A5410..5500"|"gff3tabix_genes"|"agt830.3"],1 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],2 ["ctgA%3A7000..7503"|"gff3tabix_genes"|"agt830.3"],3
+agt830.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt830.5"],1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],2 ["ctgA%3A3000..3202"|"gff3tabix_genes"|"agt830.5"],3
+an ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
+and ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
+another ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
+appear ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
+apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
+at ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
+bac ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
+bnd_a ["A%3A2700..2701"|"volvox_sv_test_renamed"|"bnd_A"],1 ["ctgA%3A2700..2701"|"volvox_sv_test"|"bnd_A"],2
+bnd_b ["A%3A34200..34201"|"volvox_sv_test_renamed"|"bnd_B"],1 ["ctgA%3A34200..34201"|"volvox_sv_test"|"bnd_B"],2
+bnd_u ["A%3A23456..23457"|"volvox_sv_test_renamed"|"bnd_U"],1 ["ctgA%3A23456..23457"|"volvox_sv_test"|"bnd_U"],2
+bnd_v ["A%3A21682..21683"|"volvox_sv_test_renamed"|"bnd_V"],1 ["ctgA%3A21682..21683"|"volvox_sv_test"|"bnd_V"],2
+bnd_w ["A%3A21681..21682"|"volvox_sv_test_renamed"|"bnd_W"],1 ["ctgA%3A21681..21682"|"volvox_sv_test"|"bnd_W"],2
+bnd_x ["A%3A23457..23458"|"volvox_sv_test_renamed"|"bnd_X"],1 ["ctgA%3A23457..23458"|"volvox_sv_test"|"bnd_X"],2
+bnd_y ["B%3A1982..1983"|"volvox_sv_test_renamed"|"bnd_Y"],1 ["ctgB%3A1982..1983"|"volvox_sv_test"|"bnd_Y"],2
+bnd_z ["B%3A1983..1984"|"volvox_sv_test_renamed"|"bnd_Z"],1 ["ctgB%3A1983..1984"|"volvox_sv_test"|"bnd_Z"],2
+both ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
+box ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
+but ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
+cds-apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
+cdss ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
+ctga ["ctgA%3A1..50001"|"gff3tabix_genes"|"ctgA"],1
+ctgb ["ctgB%3A1..6079"|"gff3tabix_genes"|"ctgB"],1
+dead ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
+eden ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],4
+eden.1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1
+eden.2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
+eden.3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
+end ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
+example ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],3 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],4
+f01 ["ctgA%3A44705..47713"|"gff3tabix_genes"|"f01"],1
+f02 ["ctgA%3A24562..28338"|"gff3tabix_genes"|"f02"],1
+f03 ["ctgA%3A36649..40440"|"gff3tabix_genes"|"f03"],1
+f04 ["ctgA%3A37242..38653"|"gff3tabix_genes"|"f04"],1
+f05 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],2
+f06 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
+f07 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
+f08 ["ctgA%3A13280..16394"|"gff3tabix_genes"|"f08"],1
+f09 ["ctgA%3A36034..38167"|"gff3tabix_genes"|"f09"],1
+f10 ["ctgA%3A15329..15533"|"gff3tabix_genes"|"f10"],1
+f11 ["ctgA%3A46990..48410"|"gff3tabix_genes"|"f11"],1
+f12 ["ctgA%3A49758..50000"|"gff3tabix_genes"|"f12"],1
+f13 ["ctgA%3A19157..22915"|"gff3tabix_genes"|"f13"],1
+f14 ["ctgA%3A23072..23185"|"gff3tabix_genes"|"f14"],1
+f15 ["ctgA%3A22132..24633"|"gff3tabix_genes"|"f15"],1
+fake ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+fakesnp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+fakesnp1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+finger ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
+fingerprinted ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
+form ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
+gene1 ["ctgA%3A1201..1500"|"single_exon_gene"|"gene1"],1
+gene2 ["ctgA%3A1201..3902"|"single_exon_gene"|"gene2"],1
+gene:hga ["ctgA%3A1100..2000"|"gff3tabix_genes"|"Gene%3Ahga"],1
+gene:hgb ["ctgA%3A1600..3000"|"gff3tabix_genes"|"Gene%3Ahgb"],1
+get ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
+helix ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],2
+hox ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
+i ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
+ig-like ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
+inv134 ["ctgA%3A2700..10000"|"volvox.inv.vcf"|"inv134"],1
+inv135 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],1 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],2
+inv9000 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv9000"],1
+is ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
+kinase ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],2 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],3 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],4 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],5
+length ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+loop ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
+m01 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
+m02 ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
+m03 ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
+m04 ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
+m05 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
+m06 ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
+m07 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],1
+m08 ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1
+m09 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],1
+m10 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],1
+m11 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],1
+m12 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],1
+m13 ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1
+m14 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],1
+m15 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],1
+match1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],1
+match2 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],1
+match3 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],1
+match4 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
+match5 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],1
+match6 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
+message. ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
+mrna ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
+mrna1 ["ctgA%3A1201..1500"|"single_exon_gene"|"mRNA1"],1
+mrna2 ["ctgA%3A1201..3902"|"single_exon_gene"|"mRNA2"],1
+no ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
+ok! ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],2
+protein ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1
+protein:hga ["ctgA%3A1200..1900"|"gff3tabix_genes"|"Protein%3AHGA"],1
+protein:hgb ["ctgA%3A1800..2900"|"gff3tabix_genes"|"Protein%3AHGB"],1
+reads ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
+remark:hga ["ctgA%3A1000..2000"|"gff3tabix_genes"|"Remark%3Ahga"],1
+repeat ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
+rna-apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
+rs1041740 ["contigA%3A11340..11341"|"volvox_test_vcf"|"rs1041740"],1
+rs10432782 ["contigA%3A7569..7570"|"volvox_test_vcf"|"rs10432782"],1
+rs112989936 ["contigA%3A10684..10685"|"volvox_test_vcf"|"rs112989936"],1
+rs114905802 ["contigA%3A4035..4036"|"volvox_test_vcf"|"rs114905802"],1
+rs11567845 ["contigA%3A8742..8743"|"volvox_test_vcf"|"rs11567845"],1
+rs116260263 ["contigA%3A6834..6835"|"volvox_test_vcf"|"rs116260263"],1
+rs117304270 ["contigA%3A11832..11833"|"volvox_test_vcf"|"rs117304270"],1
+rs117466144 ["contigA%3A11241..11242"|"volvox_test_vcf"|"rs117466144"],1
+rs118132937 ["contigA%3A9136..9137"|"volvox_test_vcf"|"rs118132937"],1
+rs16988404 ["contigA%3A7173..7174"|"volvox_test_vcf"|"rs16988404"],1
+rs17878802 ["contigA%3A5281..5282"|"volvox_test_vcf"|"rs17878802"],1
+rs17878855 ["contigA%3A3105..3106"|"volvox_test_vcf"|"rs17878855"],1
+rs17880044 ["contigA%3A11774..11775"|"volvox_test_vcf"|"rs17880044"],1
+rs17880487 ["contigA%3A12408..12409"|"volvox_test_vcf"|"rs17880487"],1
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+splice ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
+sushi ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
+that ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
+the ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
+this ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
+utrs ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
+wd40 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
+with ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],4
+zinc ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
+ああ、この機能は、世界中を旅しています！ ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],1

package/src/TrixTextSearchAdapter/test_data/volvox.ixx ADDED Viewed

	@@ -0,0 +1 @@
1	+ 1 0000000000

package/src/TrixTextSearchAdapter/test_data/volvox2_meta.json ADDED Viewed

	@@ -0,0 +1 @@
1	+ {}

package/src/TrixTextSearchAdapter/test_data/volvox_meta.json ADDED Viewed

@@ -0,0 +1,163 @@
+{
+  "dateCreated": "2022-06-17T10:57:18.370Z",
+  "tracks": [
+    {
+      "trackId": "volvox_sv_test",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.dup.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.dup.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_sv_test_renamed",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.dup.renamed.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.dup.renamed.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_test_vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.test.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.test.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "gff3tabix_genes",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "volvox.sort.gff3.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.sort.gff3.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_filtered_vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.filtered.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.filtered.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "variant_colors",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.filtered.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.filtered.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "single_exon_gene",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "single_exon_gene.sorted.gff.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "single_exon_gene.sorted.gff.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox.inv.vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.inv.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.inv.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      }
+    },
+    {
+      "trackId": "volvox.filtered.lowercase",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfAdapter",
+        "vcfLocation": {
+          "uri": "volvox.filtered.lowercase.vcf",
+          "locationType": "UriLocation"
+        }
+      }
+    }
+  ],
+  "assemblyNames": ["volvox"]
+}