@jbrowse/core 1.5.6 → 1.6.0

package/util/index.js

@@ -1,8 +1,8 @@
 "use strict";
 
-var _interopRequireWildcard = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireWildcard.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _typeof3 = require("@babel/runtime/helpers/typeof");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -54,19 +54,22 @@ var _exportNames = {
   updateStatus: true,
   hashCode: true,
   objectHash: true,
+  bytesForRegions: true,
+  viewBpToPx: true,
   SimpleFeature: true,
   isFeature: true
 };
 Object.defineProperty(exports, "SimpleFeature", {
   enumerable: true,
   get: function get() {
-    return _simpleFeature["default"];
+    return _simpleFeature.default;
   }
 });
 exports.assembleLocString = assembleLocString;
 exports.blobToDataURL = blobToDataURL;
 exports.bpSpanPx = bpSpanPx;
 exports.bpToPx = bpToPx;
+exports.bytesForRegions = bytesForRegions;
 exports.cartesianToPolar = cartesianToPolar;
 exports.clamp = clamp;
 exports.compareLocStrings = compareLocStrings;
@@ -110,20 +113,19 @@ exports.stringify = stringify;
 exports.updateStatus = updateStatus;
 exports.useDebounce = useDebounce;
 exports.useDebouncedCallback = useDebouncedCallback;
+exports.viewBpToPx = viewBpToPx;
 
-var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
-var _createForOfIteratorHelper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
-var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
-
-var _typeof2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/typeof.js"));
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -221,29 +223,42 @@ Object.keys(_offscreenCanvasUtils).forEach(function (key) {
   });
 });
 
-/* eslint-disable @typescript-eslint/no-explicit-any */
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof3(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+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; }
+
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
 if (!Object.fromEntries) {
   // @ts-ignore
-  _object["default"].shim();
+  _object.default.shim();
 }
 
-var inDevelopment = (typeof process === "undefined" ? "undefined" : (0, _typeof2["default"])(process)) === 'object' && process.env && process.env.NODE_ENV === 'development';
+var inDevelopment = (typeof process === "undefined" ? "undefined" : (0, _typeof2.default)(process)) === 'object' && process.env && process.env.NODE_ENV === 'development';
 exports.inDevelopment = inDevelopment;
 var inProduction = !inDevelopment;
 exports.inProduction = inProduction;
 
 function useDebounce(value, delay) {
   var _useState = (0, _react.useState)(value),
-      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
       debouncedValue = _useState2[0],
       setDebouncedValue = _useState2[1];
 
   (0, _react.useEffect)(function () {
-    var handler = setTimeout(function () {
+    var handle = setTimeout(function () {
       setDebouncedValue(value);
     }, delay);
     return function () {
-      clearTimeout(handler);
+      clearTimeout(handle);
     };
   }, [value, delay]);
   return debouncedValue;
@@ -278,7 +293,7 @@ function useDebouncedCallback(callback) {
 
     timeout.current = setTimeout(function () {
       if (argsRef.current) {
-        callback.apply(void 0, (0, _toConsumableArray2["default"])(argsRef.current));
+        callback.apply(void 0, (0, _toConsumableArray2.default)(argsRef.current));
       }
     }, wait);
   };
@@ -492,7 +507,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
     throw new Error("invalid location string: \"".concat(locString, "\""));
   }
 
-  var _assemblyMatch = (0, _slicedToArray2["default"])(assemblyMatch, 4),
+  var _assemblyMatch = (0, _slicedToArray2.default)(assemblyMatch, 4),
       assemblyName = _assemblyMatch[2],
       location = _assemblyMatch[3];
 
@@ -526,7 +541,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
       var singleMatch = suffix.match(/^(-?(\d+|\d{1,3}(,\d{3})*))(\.\.|-)?$/);
 
       if (rangeMatch) {
-        var _rangeMatch = (0, _slicedToArray2["default"])(rangeMatch, 6),
+        var _rangeMatch = (0, _slicedToArray2.default)(rangeMatch, 6),
             start = _rangeMatch[1],
             end = _rangeMatch[5];
 
@@ -539,7 +554,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
           };
         }
       } else if (singleMatch) {
-        var _singleMatch = (0, _slicedToArray2["default"])(singleMatch, 5),
+        var _singleMatch = (0, _slicedToArray2.default)(singleMatch, 5),
             _start = _singleMatch[1],
             separator = _singleMatch[4];
 
@@ -752,7 +767,7 @@ function iterMap(iterable, func, sizeHint) {
   var results = sizeHint ? new Array(sizeHint) : [];
   var counter = 0;
 
-  var _iterator = (0, _createForOfIteratorHelper2["default"])(iterable),
+  var _iterator = _createForOfIteratorHelper(iterable),
       _step;
 
   try {
@@ -772,7 +787,7 @@ function iterMap(iterable, func, sizeHint) {
 
 // similar to electron.js
 function mergeConfigs(A, B) {
-  var merged = (0, _deepmerge["default"])(A, B);
+  var merged = (0, _deepmerge.default)(A, B);
 
   if (B.defaultSession) {
     merged.defaultSession = B.defaultSession;
@@ -845,9 +860,9 @@ function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reacti
       return undefined;
     }
   }, /*#__PURE__*/function () {
-    var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(data, mobxReactionHandle) {
+    var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(data, mobxReactionHandle) {
       var thisInProgress, result;
-      return _index["default"].wrap(function _callee$(_context) {
+      return _regenerator.default.wrap(function _callee$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
@@ -919,16 +934,16 @@ function renameRegionIfNeeded(refNameMap, region) {
   if (region && refNameMap && refNameMap[region.refName]) {
     // clone the region so we don't modify it
     if ((0, _mobxStateTree.isStateTreeNode)(region)) {
-      region = (0, _objectSpread2["default"])({}, (0, _mobxStateTree.getSnapshot)(region));
+      region = _objectSpread({}, (0, _mobxStateTree.getSnapshot)(region));
     } else {
-      region = (0, _objectSpread2["default"])({}, region);
+      region = _objectSpread({}, region);
     } // modify it directly in the container
 
 
     var newRef = refNameMap[region.refName];
 
     if (newRef) {
-      return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, region), {}, {
+      return _objectSpread(_objectSpread({}, region), {}, {
         refName: newRef,
         originalRefName: region.refName
       });
@@ -943,10 +958,10 @@ function renameRegionsIfNeeded(_x3, _x4) {
 }
 
 function _renameRegionsIfNeeded() {
-  _renameRegionsIfNeeded = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(assemblyManager, args) {
+  _renameRegionsIfNeeded = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(assemblyManager, args) {
     var _args$regions, regions, adapterConfig, assemblyNames, assemblyMaps;
 
-    return _index["default"].wrap(function _callee3$(_context3) {
+    return _regenerator.default.wrap(function _callee3$(_context3) {
       while (1) {
         switch (_context3.prev = _context3.next) {
           case 0:
@@ -966,8 +981,8 @@ function _renameRegionsIfNeeded() {
             _context3.t0 = Object;
             _context3.next = 7;
             return Promise.all(assemblyNames.map( /*#__PURE__*/function () {
-              var _ref3 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(assemblyName) {
-                return _index["default"].wrap(function _callee2$(_context2) {
+              var _ref4 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(assemblyName) {
+                return _regenerator.default.wrap(function _callee2$(_context2) {
                   while (1) {
                     switch (_context2.prev = _context2.next) {
                       case 0:
@@ -987,17 +1002,19 @@ function _renameRegionsIfNeeded() {
                 }, _callee2);
               }));
 
-              return function (_x8) {
-                return _ref3.apply(this, arguments);
+              return function (_x10) {
+                return _ref4.apply(this, arguments);
               };
             }()));
 
           case 7:
             _context3.t1 = _context3.sent;
             assemblyMaps = _context3.t0.fromEntries.call(_context3.t0, _context3.t1);
-            return _context3.abrupt("return", (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, args), {}, {
-              regions: regions.map(function (region) {
-                return renameRegionIfNeeded(assemblyMaps[region.assemblyName], region);
+            return _context3.abrupt("return", _objectSpread(_objectSpread({}, args), {}, {
+              regions: regions.map(function (region, i) {
+                return (// note: uses assemblyNames defined above since region could be dead now
+                  renameRegionIfNeeded(assemblyMaps[assemblyNames[i]], region)
+                );
               })
             }));
 
@@ -1236,9 +1253,9 @@ function updateStatus(_x5, _x6, _x7) {
 }
 
 function _updateStatus() {
-  _updateStatus = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4(statusMsg, statusCallback, fn) {
+  _updateStatus = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(statusMsg, statusCallback, fn) {
     var result;
-    return _index["default"].wrap(function _callee4$(_context4) {
+    return _regenerator.default.wrap(function _callee4$(_context4) {
       while (1) {
         switch (_context4.prev = _context4.next) {
           case 0:
@@ -1279,4 +1296,81 @@ function hashCode(str) {
 
 function objectHash(obj) {
   return "".concat(hashCode(JSON.stringify(obj)));
+}
+
+function bytesForRegions(_x8, _x9) {
+  return _bytesForRegions.apply(this, arguments);
+}
+
+function _bytesForRegions() {
+  _bytesForRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(regions, index) {
+    var blockResults;
+    return _regenerator.default.wrap(function _callee5$(_context5) {
+      while (1) {
+        switch (_context5.prev = _context5.next) {
+          case 0:
+            _context5.next = 2;
+            return Promise.all(regions.map(function (r) {
+              return index.blocksForRange(r.refName, r.start, r.end);
+            }));
+
+          case 2:
+            blockResults = _context5.sent;
+            return _context5.abrupt("return", blockResults.flat().map(function (block) {
+              return {
+                start: block.minv.blockPosition,
+                end: block.maxv.blockPosition + 65535
+              };
+            }).reduce(function (a, b) {
+              return a + b.end - b.start;
+            }, 0));
+
+          case 4:
+          case "end":
+            return _context5.stop();
+        }
+      }
+    }, _callee5);
+  }));
+  return _bytesForRegions.apply(this, arguments);
+}
+
+function viewBpToPx(_ref3) {
+  var refName = _ref3.refName,
+      coord = _ref3.coord,
+      regionNumber = _ref3.regionNumber,
+      self = _ref3.self;
+  var offsetBp = 0;
+  var interRegionPaddingBp = self.interRegionPaddingWidth * self.bpPerPx;
+  var minimumBlockBp = self.minimumBlockWidth * self.bpPerPx;
+  var index = self.displayedRegions.findIndex(function (region, idx) {
+    var len = region.end - region.start;
+
+    if (refName === region.refName && coord >= region.start && coord <= region.end) {
+      if (regionNumber ? regionNumber === idx : true) {
+        offsetBp += region.reversed ? region.end - coord : coord - region.start;
+        return true;
+      }
+    } // add the interRegionPaddingWidth if the boundary is in the screen
+    // e.g. offset>=0 && offset<width
+
+
+    if (len > minimumBlockBp && offsetBp / self.bpPerPx >= 0 && offsetBp / self.bpPerPx < self.width) {
+      offsetBp += len + interRegionPaddingBp;
+    } else {
+      offsetBp += len;
+    }
+
+    return false;
+  });
+  var foundRegion = self.displayedRegions[index];
+
+  if (foundRegion) {
+    return {
+      index: index,
+      offsetPx: Math.round(offsetBp / self.bpPerPx)
+    };
+  }
+
+  return undefined;
 }

package/util/index.test.js

@@ -1,13 +1,17 @@
 "use strict";
 
-var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
 var _index = require("./index");
 
+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; }
+
 describe('parseLocString', function () {
   var cases = [['chr1:1..200', {
     start: 0,
@@ -66,7 +70,7 @@ describe('parseLocString', function () {
     refName: 'chr1'
   }]];
   cases.forEach(function (_ref) {
-    var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
+    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
         input = _ref2[0],
         output = _ref2[1];
 
@@ -114,7 +118,7 @@ describe('assembleLocString', function () {
     refName: 'chr1'
   }, 'chr1:-99..-1']];
   cases.forEach(function (_ref3) {
-    var _ref4 = (0, _slicedToArray2["default"])(_ref3, 2),
+    var _ref4 = (0, _slicedToArray2.default)(_ref3, 2),
         input = _ref4[0],
         output = _ref4[1];
 
@@ -147,7 +151,7 @@ describe('assembleLocString', function () {
   test("assemble and parse 'chr1:1..100'", function () {
     expect((0, _index.parseLocString)((0, _index.assembleLocString)(location), function (refName) {
       return refName === 'chr1' || refName === 'chr2';
-    })).toEqual((0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, location), {}, {
+    })).toEqual(_objectSpread(_objectSpread({}, location), {}, {
       start: 0
     }));
   });
@@ -155,7 +159,7 @@ describe('assembleLocString', function () {
 describe('compareLocStrings', function () {
   var cases = [['chr1:1..200', 'chr1:1-200', 0], ['chr1:1-200', '{hg19}chr1:1-200', -1], ['{hg19}chr1:1-200', 'chr1:1-200', 1], ['{hg19}chr1:1-200', '{hg19}chr1:2-200', -1]];
   cases.forEach(function (_ref5) {
-    var _ref6 = (0, _slicedToArray2["default"])(_ref5, 3),
+    var _ref6 = (0, _slicedToArray2.default)(_ref5, 3),
         input1 = _ref6[0],
         input2 = _ref6[1],
         output = _ref6[2];

package/util/io/RemoteFileWithRangeCache.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -8,27 +8,25 @@ Object.defineProperty(exports, "__esModule", {
 exports.RemoteFileWithRangeCache = void 0;
 exports.clearCache = clearCache;
 
-var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _createForOfIteratorHelper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
-var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
-var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
-var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
+var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
 
-var _get2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/get.js"));
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
 
-var _getPrototypeOf2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/getPrototypeOf.js"));
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
 
-var _inherits2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/inherits.js"));
-
-var _createSuper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
 
 var _httpRangeFetcher = require("http-range-fetcher");
 
@@ -36,6 +34,20 @@ var _buffer = require("buffer");
 
 var _genericFilehandle = require("generic-filehandle");
 
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
+
+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; }
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
 var fetchers = {};
 
 function binaryRangeFetch(url, start, end) {
@@ -66,22 +78,22 @@ function clearCache() {
 }
 
 var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
-  (0, _inherits2["default"])(RemoteFileWithRangeCache, _RemoteFile);
+  (0, _inherits2.default)(RemoteFileWithRangeCache, _RemoteFile);
 
-  var _super = (0, _createSuper2["default"])(RemoteFileWithRangeCache);
+  var _super = _createSuper(RemoteFileWithRangeCache);
 
   function RemoteFileWithRangeCache() {
-    (0, _classCallCheck2["default"])(this, RemoteFileWithRangeCache);
+    (0, _classCallCheck2.default)(this, RemoteFileWithRangeCache);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(RemoteFileWithRangeCache, [{
+  (0, _createClass2.default)(RemoteFileWithRangeCache, [{
     key: "fetch",
     value: function () {
-      var _fetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(url, init) {
+      var _fetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, init) {
         var requestHeaders, range, _ref, _ref2, rangeParse, _rangeParse, _start, _end, s, e, response, headers;
 
-        return _index["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -98,12 +110,12 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                   } else if (Array.isArray(requestHeaders)) {
                     ;
                     _ref = requestHeaders.find(function (_ref3) {
-                      var _ref4 = (0, _slicedToArray2["default"])(_ref3, 1),
+                      var _ref4 = (0, _slicedToArray2.default)(_ref3, 1),
                           key = _ref4[0];
 
                       return key === 'range';
                     }) || [undefined, undefined];
-                    _ref2 = (0, _slicedToArray2["default"])(_ref, 2);
+                    _ref2 = (0, _slicedToArray2.default)(_ref, 2);
                     range = _ref2[1];
                   } else {
                     range = requestHeaders.range;
@@ -122,7 +134,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                   break;
                 }
 
-                _rangeParse = (0, _slicedToArray2["default"])(rangeParse, 3), _start = _rangeParse[1], _end = _rangeParse[2];
+                _rangeParse = (0, _slicedToArray2.default)(rangeParse, 3), _start = _rangeParse[1], _end = _rangeParse[2];
                 s = parseInt(_start, 10);
                 e = parseInt(_end, 10);
                 _context.next = 11;
@@ -139,7 +151,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                 }));
 
               case 14:
-                return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, init));
+                return _context.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, init));
 
               case 15:
               case "end":
@@ -158,7 +170,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
   }, {
     key: "fetchBinaryRange",
     value: function () {
-      var _fetchBinaryRange = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(url, start, end) {
+      var _fetchBinaryRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(url, start, end) {
         var options,
             requestDate,
             requestHeaders,
@@ -175,17 +187,17 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
             arrayBuffer,
             _args2 = arguments;
 
-        return _index["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
                 options = _args2.length > 3 && _args2[3] !== undefined ? _args2[3] : {};
                 requestDate = new Date();
-                requestHeaders = (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, options.headers), {}, {
+                requestHeaders = _objectSpread(_objectSpread({}, options.headers), {}, {
                   range: "bytes=".concat(start, "-").concat(end)
                 });
                 _context2.next = 5;
-                return (0, _get2["default"])((0, _getPrototypeOf2["default"])(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, options), {}, {
+                return (0, _get2.default)((0, _getPrototypeOf2.default)(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, _objectSpread(_objectSpread({}, options), {}, {
                   headers: requestHeaders
                 }));
 
@@ -207,11 +219,11 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                 // will miss duplicate headers of course
                 // eslint-disable-next-line @typescript-eslint/no-explicit-any
                 headers = {};
-                _iterator = (0, _createForOfIteratorHelper2["default"])(res.headers.entries());
+                _iterator = _createForOfIteratorHelper(res.headers.entries());
 
                 try {
                   for (_iterator.s(); !(_step = _iterator.n()).done;) {
-                    _step$value = (0, _slicedToArray2["default"])(_step.value, 2), k = _step$value[0], v = _step$value[1];
+                    _step$value = (0, _slicedToArray2.default)(_step.value, 2), k = _step$value[0], v = _step$value[1];
                     headers[k] = v;
                   } // return the response headers, and the data buffer
 

package/util/io/index.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -13,9 +13,9 @@ Object.defineProperty(exports, "RemoteFileWithRangeCache", {
 });
 exports.openLocation = openLocation;
 
-var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _genericFilehandle = require("generic-filehandle");
 
@@ -41,9 +41,9 @@ function openLocation(location, pluginManager) {
   }
 
   function _checkAuthNeededFetch() {
-    _checkAuthNeededFetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(url, opts) {
+    _checkAuthNeededFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, opts) {
       var response, authHeaders;
-      return _index["default"].wrap(function _callee$(_context) {
+      return _regenerator.default.wrap(function _callee$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
@@ -89,7 +89,7 @@ function openLocation(location, pluginManager) {
       throw new Error('No local path provided');
     }
 
-    if (_detectNode["default"]) {
+    if (_detectNode.default) {
       return new _genericFilehandle.LocalFile(location.localPath);
     } else {
       throw new Error("can't use local files in the browser");

package/util/jexl.js

@@ -1,18 +1,18 @@
 "use strict";
 
-var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = _default;
+exports.default = _default;
 
 var _jexl = _interopRequireDefault(require("jexl"));
 
 function
   /* config?: any*/
 _default() {
-  var j = new _jexl["default"].Jexl(); // someday will make sure all of configs callbacks are added in, including
+  var j = new _jexl.default.Jexl(); // someday will make sure all of configs callbacks are added in, including
   // ones passed in
   // below are core functions
 
@@ -49,8 +49,8 @@ _default() {
   j.addFunction('parseInt', Number.parseInt);
   j.addFunction('parseFloat', Number.parseFloat); // string
 
-  j.addFunction('split', function (str, _char) {
-    return str.split(_char);
+  j.addFunction('split', function (str, char) {
+    return str.split(char);
   });
   j.addFunction('charAt', function (str, index) {
     return str.charAt(index);