@jbrowse/plugin-legacy-jbrowse 1.7.11 → 2.0.0

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -1,179 +1,191 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.parseJB1Conf = parseJB1Conf;
-exports.parseJB1Json = parseJB1Json;
-exports.regularizeConf = regularizeConf;
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _getValue = _interopRequireDefault(require("get-value"));
-
-var _setValue = _interopRequireDefault(require("set-value"));
-
-var _util = require("@jbrowse/core/util");
-
-var _util2 = require("./util");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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 __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.regularizeConf = exports.parseJB1Conf = exports.parseJB1Json = void 0;
+/* eslint no-cond-assign: ["error", "except-parens"] */
+var get_value_1 = __importDefault(require("get-value"));
+var set_value_1 = __importDefault(require("set-value"));
+var util_1 = require("@jbrowse/core/util");
+var util_2 = require("./util");
 function parseJB1Json(config, url) {
-  if (typeof config === 'string') {
+    if (typeof config === 'string') {
+        var parsedConf = void 0;
+        try {
+            parsedConf = JSON.parse(config);
+        }
+        catch (error) {
+            throw new Error("".concat(error, " when parsing configuration."));
+        }
+        return regularizeConf(parsedConf, url);
+    }
+    return regularizeConf(config, url);
+}
+exports.parseJB1Json = parseJB1Json;
+function parseJB1Conf(config, url) {
     var parsedConf;
-
     try {
-      parsedConf = JSON.parse(config);
-    } catch (error) {
-      throw new Error("".concat(error, " when parsing configuration."));
+        parsedConf = parse(config, url);
+    }
+    catch (error) {
+        throw new Error("".concat(error, " when parsing configuration."));
     }
-
     return regularizeConf(parsedConf, url);
-  }
-
-  return regularizeConf(config, url);
-}
-
-function parseJB1Conf(config, url) {
-  var parsedConf;
-
-  try {
-    parsedConf = parse(config, url);
-  } catch (error) {
-    throw new Error("".concat(error, " when parsing configuration."));
-  }
-
-  return regularizeConf(parsedConf, url);
 }
-
+exports.parseJB1Conf = parseJB1Conf;
 function isAlwaysArray(varName) {
-  if (varName === 'include') {
-    return true;
-  }
-
-  return false;
+    if (varName === 'include') {
+        return true;
+    }
+    return false;
 }
-
 function parse(text, url) {
-  var section = [];
-  var keyPath;
-  var operation;
-  var value;
-  var data = {
-    tracks: {}
-  };
-  var lineNumber;
-
-  function recordVal() {
-    if (value !== undefined) {
-      var parsedValue;
-
-      try {
-        // parse json
-        var match = value.match(/^json:(.+)/i);
-
-        if (match) {
-          parsedValue = JSON.parse(match[1]);
-        } // parse numbers if it looks numeric
-        else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-          parsedValue = parseFloat(value.replace(/,/g, ''));
-        } else {
-          parsedValue = value;
+    var section = [];
+    var keyPath;
+    var operation;
+    var value;
+    var data = { tracks: {} };
+    var lineNumber;
+    function recordVal() {
+        if (value !== undefined) {
+            var parsedValue = void 0;
+            try {
+                // parse json
+                var match = value.match(/^json:(.+)/i);
+                if (match) {
+                    parsedValue = JSON.parse(match[1]);
+                }
+                // parse numbers if it looks numeric
+                else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
+                    parsedValue = parseFloat(value.replace(/,/g, ''));
+                }
+                else {
+                    parsedValue = value;
+                }
+                if (!keyPath) {
+                    throw new Error("Error parsing in section ".concat(section.join(' - ')));
+                }
+                var path = section.concat(keyPath).join('.');
+                if (operation === '+=') {
+                    var existing = (0, get_value_1.default)(data, path);
+                    if (existing) {
+                        if (!Array.isArray(existing)) {
+                            existing = [existing];
+                        }
+                    }
+                    else {
+                        existing = [];
+                    }
+                    existing.push(parsedValue);
+                    parsedValue = existing;
+                }
+                if (parsedValue === 'true') {
+                    parsedValue = true;
+                }
+                if (parsedValue === 'false') {
+                    parsedValue = false;
+                }
+                (0, set_value_1.default)(data, path, parsedValue);
+            }
+            catch (e) {
+                throw new Error("syntax error".concat(url ? " in ".concat(url) : '').concat(lineNumber ? " at line ".concat(lineNumber - 1) : ''));
+            }
         }
-
-        if (!keyPath) {
-          throw new Error("Error parsing in section ".concat(section.join(' - ')));
+    }
+    text.split('\n').forEach(function (textLine, i) {
+        var _a;
+        lineNumber = i + 1;
+        var line = textLine.replace(/^\s*#.+/, '');
+        // new section
+        var match;
+        if ((match = line.match(/^\s*\[([^\]]+)/))) {
+            // new section
+            recordVal();
+            keyPath = undefined;
+            value = undefined;
+            section = match[1].trim().split(/\s*\.\s*/);
+            if (section.length === 1 && section[0].toLowerCase() === 'general') {
+                section = [];
+            }
         }
-
-        var path = section.concat(keyPath).join('.');
-
-        if (operation === '+=') {
-          var existing = (0, _getValue.default)(data, path);
-
-          if (existing) {
-            if (!Array.isArray(existing)) {
-              existing = [existing];
+        // new value
+        else if ((match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))) {
+            recordVal();
+            keyPath = match[1].trim().split(/\s*\.\s*/);
+            _a = __read(match, 3), operation = _a[2];
+            if (isAlwaysArray(section.concat(keyPath).join('.'))) {
+                operation = '+=';
             }
-          } else {
-            existing = [];
-          }
-
-          existing.push(parsedValue);
-          parsedValue = existing;
+            value = match[3].trim();
         }
-
-        if (parsedValue === 'true') {
-          parsedValue = true;
+        // add to existing array value
+        else if (keyPath !== undefined &&
+            (match = line.match(/^\s{0,4}\+\s*(.+)/))) {
+            recordVal();
+            operation = '+=';
+            value = match[1].trim();
         }
-
-        if (parsedValue === 'false') {
-          parsedValue = false;
+        // add to existing value
+        else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
+            value += value.length ? " ".concat(match[1].trim()) : match[1].trim();
         }
-
-        (0, _setValue.default)(data, path, parsedValue);
-      } catch (e) {
-        throw new Error("syntax error".concat(url ? " in ".concat(url) : '').concat(lineNumber ? " at line ".concat(lineNumber - 1) : ''));
-      }
-    }
-  }
-
-  text.split('\n').forEach(function (textLine, i) {
-    lineNumber = i + 1;
-    var line = textLine.replace(/^\s*#.+/, ''); // new section
-
-    var match;
-
-    if (match = line.match(/^\s*\[([^\]]+)/)) {
-      // new section
-      recordVal();
-      keyPath = undefined;
-      value = undefined;
-      section = match[1].trim().split(/\s*\.\s*/);
-
-      if (section.length === 1 && section[0].toLowerCase() === 'general') {
-        section = [];
-      }
-    } // new value
-    else if (match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/)) {
-      recordVal();
-      keyPath = match[1].trim().split(/\s*\.\s*/);
-      var _match = match;
-
-      var _match2 = (0, _slicedToArray2.default)(_match, 3);
-
-      operation = _match2[2];
-
-      if (isAlwaysArray(section.concat(keyPath).join('.'))) {
-        operation = '+=';
-      }
-
-      value = match[3].trim();
-    } // add to existing array value
-    else if (keyPath !== undefined && (match = line.match(/^\s{0,4}\+\s*(.+)/))) {
-      recordVal();
-      operation = '+=';
-      value = match[1].trim();
-    } // add to existing value
-    else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
-      value += value.length ? " ".concat(match[1].trim()) : match[1].trim();
-    } // done with last value
-    else {
-      recordVal();
-      keyPath = undefined;
-      value = undefined;
-    }
-  });
-  recordVal();
-  return data;
+        // done with last value
+        else {
+            recordVal();
+            keyPath = undefined;
+            value = undefined;
+        }
+    });
+    recordVal();
+    return data;
 }
 /**
  * Applies defaults and any other necessary tweaks to the loaded configuration.
@@ -182,295 +194,262 @@ function parse(text, url) {
  * @param url - URL of the config file
  * @returns the same object it was passed
  */
-
-
 function regularizeConf(conf, url) {
-  // if tracks is not an array, convert it to one
-  if (conf.tracks && !Array.isArray(conf.tracks)) {
-    // if it's a single track config, wrap it in an arrayref
-    if ((0, _util2.isTrack)(conf.tracks)) {
-      conf.tracks = [conf.tracks];
-    } // otherwise, coerce it to an array
-    else {
-      var tracks = [];
-
-      for (var _i = 0, _Object$keys = Object.keys(conf.tracks); _i < _Object$keys.length; _i++) {
-        var label = _Object$keys[_i];
-        var track = conf.tracks[label];
-
-        if ((0, _util2.isTrack)(track)) {
-          tracks.push(track);
-        } else {
-          tracks.push(_objectSpread({
-            label: label
-          }, track));
+    var e_1, _a, e_2, _b;
+    // if tracks is not an array, convert it to one
+    if (conf.tracks && !Array.isArray(conf.tracks)) {
+        // if it's a single track config, wrap it in an arrayref
+        if ((0, util_2.isTrack)(conf.tracks)) {
+            conf.tracks = [conf.tracks];
+        }
+        // otherwise, coerce it to an array
+        else {
+            var tracks = [];
+            try {
+                for (var _c = __values(Object.keys(conf.tracks)), _d = _c.next(); !_d.done; _d = _c.next()) {
+                    var label = _d.value;
+                    var track = conf.tracks[label];
+                    if ((0, util_2.isTrack)(track)) {
+                        tracks.push(track);
+                    }
+                    else {
+                        tracks.push(__assign({ label: label }, track));
+                    }
+                }
+            }
+            catch (e_1_1) { e_1 = { error: e_1_1 }; }
+            finally {
+                try {
+                    if (_d && !_d.done && (_a = _c.return)) _a.call(_c);
+                }
+                finally { if (e_1) throw e_1.error; }
+            }
+            conf.tracks = tracks;
+        }
+    }
+    // regularize trackMetadata.sources
+    var meta = conf.trackMetadata;
+    if (meta && meta.sources) {
+        // if it's a single source config, wrap it in an arrayref
+        if (typeof meta.sources === 'string') {
+            meta.sources = [meta.sources];
         }
-      }
-
-      conf.tracks = tracks;
-    }
-  } // regularize trackMetadata.sources
-
-
-  var meta = conf.trackMetadata;
-
-  if (meta && meta.sources) {
-    // if it's a single source config, wrap it in an arrayref
-    if (typeof meta.sources === 'string') {
-      meta.sources = [meta.sources];
-    }
-
-    if ((0, _util2.isSource)(meta.sources)) {
-      meta.sources = [meta.sources];
-    }
-
-    if (!Array.isArray(meta.sources)) {
-      var sources = [];
-
-      for (var _i2 = 0, _Object$keys2 = Object.keys(meta.sources); _i2 < _Object$keys2.length; _i2++) {
-        var name = _Object$keys2[_i2];
-        var source = meta.sources[name];
-
-        if (!('name' in source)) {
-          source.name = name;
+        if ((0, util_2.isSource)(meta.sources)) {
+            meta.sources = [meta.sources];
+        }
+        if (!Array.isArray(meta.sources)) {
+            var sources = [];
+            try {
+                for (var _e = __values(Object.keys(meta.sources)), _f = _e.next(); !_f.done; _f = _e.next()) {
+                    var name_1 = _f.value;
+                    var source = meta.sources[name_1];
+                    if (!('name' in source)) {
+                        source.name = name_1;
+                    }
+                    sources.push(source);
+                }
+            }
+            catch (e_2_1) { e_2 = { error: e_2_1 }; }
+            finally {
+                try {
+                    if (_f && !_f.done && (_b = _e.return)) _b.call(_e);
+                }
+                finally { if (e_2) throw e_2.error; }
+            }
+            meta.sources = sources;
+        }
+        // coerce any string source defs to be URLs, and try to detect their types
+        meta.sources = meta.sources.map(function (sourceDef) {
+            if (typeof sourceDef === 'string') {
+                var newSourceDef = { url: sourceDef };
+                var typeMatch = sourceDef.match(/\.(\w+)$/);
+                if (typeMatch) {
+                    newSourceDef.type = typeMatch[1].toLowerCase();
+                }
+                return newSourceDef;
+            }
+            return sourceDef;
+        });
+    }
+    conf.sourceUrl = conf.sourceUrl || url;
+    if (conf.sourceUrl.startsWith('/')) {
+        conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href;
+    }
+    conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href;
+    if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {
+        conf.baseUrl += '/';
+    }
+    if (conf.sourceUrl) {
+        // set a default baseUrl in each of the track and store confs, and the names
+        // conf, if needed
+        var addBase = [];
+        if (conf.tracks) {
+            addBase.push.apply(addBase, __spreadArray([], __read(conf.tracks), false));
         }
-
-        sources.push(source);
-      }
-
-      meta.sources = sources;
-    } // coerce any string source defs to be URLs, and try to detect their types
-
-
-    meta.sources = meta.sources.map(function (sourceDef) {
-      if (typeof sourceDef === 'string') {
-        var newSourceDef = {
-          url: sourceDef
-        };
-        var typeMatch = sourceDef.match(/\.(\w+)$/);
-
-        if (typeMatch) {
-          newSourceDef.type = typeMatch[1].toLowerCase();
+        if (conf.stores) {
+            addBase.push.apply(addBase, __spreadArray([], __read(Object.values(conf.stores)), false));
+        }
+        if (conf.names) {
+            addBase.push(conf.names);
+        }
+        addBase.forEach(function (t) {
+            if (!t.baseUrl) {
+                t.baseUrl = conf.baseUrl || '/';
+            }
+        });
+        // resolve the refSeqs and nameUrl if present
+        if (conf.refSeqs && typeof conf.refSeqs === 'string') {
+            conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href;
+        }
+        if (conf.nameUrl) {
+            conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href;
+        }
+    }
+    conf.stores = conf.stores || {};
+    (conf.tracks || []).forEach(function (trackConfig) {
+        // if there is a `config` subpart, just copy its keys in to the top-level
+        // config
+        if (trackConfig.config) {
+            var c = trackConfig.config;
+            delete trackConfig.config;
+            trackConfig = __assign(__assign({}, c), trackConfig);
+        }
+        // skip if it's a new-style track def
+        if (trackConfig.store) {
+            return;
+        }
+        var trackClassName;
+        if (trackConfig.type === 'FeatureTrack') {
+            trackClassName = 'JBrowse/View/Track/HTMLFeatures';
+        }
+        else if (trackConfig.type === 'ImageTrack') {
+            trackClassName = 'JBrowse/View/Track/FixedImage';
+        }
+        else if (trackConfig.type === 'ImageTrack.Wiggle') {
+            trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle';
+        }
+        else if (trackConfig.type === 'SequenceTrack') {
+            trackClassName = 'JBrowse/View/Track/Sequence';
+        }
+        else {
+            trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type);
+        }
+        trackConfig.type = trackClassName;
+        synthesizeTrackStoreConfig(conf, trackConfig);
+        if (trackConfig.histograms) {
+            if (!trackConfig.histograms.baseUrl) {
+                trackConfig.histograms.baseUrl = trackConfig.baseUrl;
+            }
+            synthesizeTrackStoreConfig(conf, trackConfig.histograms);
         }
-
-        return newSourceDef;
-      }
-
-      return sourceDef;
     });
-  }
-
-  conf.sourceUrl = conf.sourceUrl || url;
-
-  if (conf.sourceUrl.startsWith('/')) {
-    conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href;
-  }
-
-  conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href;
-
-  if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {
-    conf.baseUrl += '/';
-  }
-
-  if (conf.sourceUrl) {
-    // set a default baseUrl in each of the track and store confs, and the names
-    // conf, if needed
-    var addBase = [];
-
-    if (conf.tracks) {
-      addBase.push.apply(addBase, (0, _toConsumableArray2.default)(conf.tracks));
-    }
-
-    if (conf.stores) {
-      addBase.push.apply(addBase, (0, _toConsumableArray2.default)(Object.values(conf.stores)));
-    }
-
-    if (conf.names) {
-      addBase.push(conf.names);
-    }
-
-    addBase.forEach(function (t) {
-      if (!t.baseUrl) {
-        t.baseUrl = conf.baseUrl || '/';
-      }
-    }); // resolve the refSeqs and nameUrl if present
-
-    if (conf.refSeqs && typeof conf.refSeqs === 'string') {
-      conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href;
-    }
-
-    if (conf.nameUrl) {
-      conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href;
-    }
-  }
-
-  conf.stores = conf.stores || {};
-  (conf.tracks || []).forEach(function (trackConfig) {
-    // if there is a `config` subpart, just copy its keys in to the top-level
-    // config
-    if (trackConfig.config) {
-      var c = trackConfig.config;
-      delete trackConfig.config;
-      trackConfig = _objectSpread(_objectSpread({}, c), trackConfig);
-    } // skip if it's a new-style track def
-
-
-    if (trackConfig.store) {
-      return;
-    }
-
-    var trackClassName;
-
-    if (trackConfig.type === 'FeatureTrack') {
-      trackClassName = 'JBrowse/View/Track/HTMLFeatures';
-    } else if (trackConfig.type === 'ImageTrack') {
-      trackClassName = 'JBrowse/View/Track/FixedImage';
-    } else if (trackConfig.type === 'ImageTrack.Wiggle') {
-      trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle';
-    } else if (trackConfig.type === 'SequenceTrack') {
-      trackClassName = 'JBrowse/View/Track/Sequence';
-    } else {
-      trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type);
-    }
-
-    trackConfig.type = trackClassName;
-    synthesizeTrackStoreConfig(conf, trackConfig);
-
-    if (trackConfig.histograms) {
-      if (!trackConfig.histograms.baseUrl) {
-        trackConfig.histograms.baseUrl = trackConfig.baseUrl;
-      }
-
-      synthesizeTrackStoreConfig(conf, trackConfig.histograms);
-    }
-  });
-  return conf;
+    return conf;
 }
+exports.regularizeConf = regularizeConf;
 /**
  * prefix class name with `root` if it contains no slashes
  * @param root - Prefix root
  * @param className - class name
  */
-
-
 function regularizeClass(root, className) {
-  if (!className) {
-    return '';
-  }
-
-  if (!className.includes('/')) {
-    className = "".concat(root, "/").concat(className);
-  }
-
-  className = className.replace(/^\//, '');
-  return className;
+    if (!className) {
+        return '';
+    }
+    if (!className.includes('/')) {
+        className = "".concat(root, "/").concat(className);
+    }
+    className = className.replace(/^\//, '');
+    return className;
 }
-
 function guessStoreClass(trackConfig, urlTemplate) {
-  if (!trackConfig) {
+    if (!trackConfig) {
+        return '';
+    }
+    if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
+        return "JBrowse/Store/TiledImage/Fixed".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
+    }
+    if (/\.jsonz?$/i.test(urlTemplate)) {
+        return "JBrowse/Store/SeqFeature/NCList".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
+    }
+    if (/\.bam$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BAM';
+    }
+    if (/\.cram$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/CRAM';
+    }
+    if (/\.gff3?$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/GFF3';
+    }
+    if (/\.bed$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BED';
+    }
+    if (/\.vcf.b?gz$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/VCFTabix';
+    }
+    if (/\.gff3?.b?gz$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/GFF3Tabix';
+    }
+    if (/\.bed.b?gz$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BEDTabix';
+    }
+    if (/\.(bw|bigwig)$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BigWig';
+    }
+    if (/\.(bb|bigbed)$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BigBed';
+    }
+    if (/\.(fa|fasta)$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/IndexedFasta';
+    }
+    if (/\.(fa|fasta)\.b?gz$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta';
+    }
+    if (/\.2bit$/i.test(urlTemplate)) {
+        return 'JBrowse/Store/SeqFeature/TwoBit';
+    }
+    if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
+        return 'JBrowse/Store/Sequence/StaticChunked';
+    }
     return '';
-  }
-
-  if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
-    return "JBrowse/Store/TiledImage/Fixed".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
-  }
-
-  if (/\.jsonz?$/i.test(urlTemplate)) {
-    return "JBrowse/Store/SeqFeature/NCList".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
-  }
-
-  if (/\.bam$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BAM';
-  }
-
-  if (/\.cram$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/CRAM';
-  }
-
-  if (/\.gff3?$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/GFF3';
-  }
-
-  if (/\.bed$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BED';
-  }
-
-  if (/\.vcf.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/VCFTabix';
-  }
-
-  if (/\.gff3?.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/GFF3Tabix';
-  }
-
-  if (/\.bed.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BEDTabix';
-  }
-
-  if (/\.(bw|bigwig)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BigWig';
-  }
-
-  if (/\.(bb|bigbed)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BigBed';
-  }
-
-  if (/\.(fa|fasta)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/IndexedFasta';
-  }
-
-  if (/\.(fa|fasta)\.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta';
-  }
-
-  if (/\.2bit$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/TwoBit';
-  }
-
-  if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
-    return 'JBrowse/Store/Sequence/StaticChunked';
-  }
-
-  return '';
 }
-
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
-  // figure out what data store class to use with the track, applying some
-  // defaults if it is not explicit in the configuration
-  var _trackConfig$urlTempl = trackConfig.urlTemplate,
-      urlTemplate = _trackConfig$urlTempl === void 0 ? '' : _trackConfig$urlTempl;
-  var storeClass;
-
-  if (trackConfig.storeClass) {
-    storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass);
-  } else {
-    storeClass = guessStoreClass(trackConfig, urlTemplate);
-  }
-
-  if (!storeClass) {
-    console.warn("Unable to determine an appropriate data store to use with track '".concat(trackConfig.label, "', please explicitly specify a storeClass in the configuration."));
-    return;
-  } // synthesize a separate store conf
-
-
-  var storeConf = _objectSpread(_objectSpread({}, trackConfig), {}, {
-    type: storeClass
-  }); // if this is the first sequence store we see, and we have no refseqs store
-  // defined explicitly, make this the refseqs store.
-
-
-  if ((storeClass === 'JBrowse/Store/Sequence/StaticChunked' || storeClass === 'JBrowse/Store/Sequence/IndexedFasta' || storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' || storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' || storeClass === 'JBrowse/Store/SeqFeature/TwoBit' || storeClass === 'JBrowse/Store/Sequence/TwoBit' || trackConfig.useAsRefSeqStore) && !(mainConf.stores && mainConf.stores.refseqs)) {
-    storeConf.name = 'refseqs';
-  } else {
-    storeConf.name = "store".concat((0, _util.objectHash)(storeConf));
-  } // record it
-
-
-  if (!mainConf.stores) {
-    mainConf.stores = {};
-  }
-
-  mainConf.stores[storeConf.name] = storeConf; // connect it to the track conf
-
-  trackConfig.store = storeConf.name;
-}
+    // figure out what data store class to use with the track, applying some
+    // defaults if it is not explicit in the configuration
+    var _a = trackConfig.urlTemplate, urlTemplate = _a === void 0 ? '' : _a;
+    var storeClass;
+    if (trackConfig.storeClass) {
+        storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass);
+    }
+    else {
+        storeClass = guessStoreClass(trackConfig, urlTemplate);
+    }
+    if (!storeClass) {
+        console.warn("Unable to determine an appropriate data store to use with track '".concat(trackConfig.label, "', please explicitly specify a storeClass in the configuration."));
+        return;
+    }
+    // synthesize a separate store conf
+    var storeConf = __assign(__assign({}, trackConfig), { type: storeClass });
+    // if this is the first sequence store we see, and we have no refseqs store
+    // defined explicitly, make this the refseqs store.
+    if ((storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
+        storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
+        storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
+        storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||
+        storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
+        storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
+        trackConfig.useAsRefSeqStore) &&
+        !(mainConf.stores && mainConf.stores.refseqs)) {
+        storeConf.name = 'refseqs';
+    }
+    else {
+        storeConf.name = "store".concat((0, util_1.objectHash)(storeConf));
+    }
+    // record it
+    if (!mainConf.stores) {
+        mainConf.stores = {};
+    }
+    mainConf.stores[storeConf.name] = storeConf;
+    // connect it to the track conf
+    trackConfig.store = storeConf.name;
+}
+//# sourceMappingURL=jb1ConfigParse.js.map