@jbrowse/plugin-bed 1.6.8 → 1.7.1

package/dist/index.js

@@ -1,8 +1,137 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-bed.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-bed.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _BigBedAdapter = require("./BigBedAdapter");
+
+var _BedTabixAdapter = require("./BedTabixAdapter");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+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 || _typeof(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 _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 BedPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(BedPlugin, _Plugin);
+
+  var _super = _createSuper(BedPlugin);
+
+  function BedPlugin() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, BedPlugin);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'BedPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(BedPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'BigBedAdapter',
+          configSchema: _BigBedAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./BigBedAdapter/BigBedAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(bb|bigbed)$/i;
+          var adapterName = 'BigBedAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            bigBedLocation: file
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'BedTabixAdapter',
+          configSchema: _BedTabixAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./BedTabixAdapter/BedTabixAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.bed\.b?gz$/i;
+          var adapterName = 'BedTabixAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var indexName = index && (0, _tracks.getFileName)(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedGzLocation: file,
+              index: {
+                location: index || (0, _tracks.makeIndex)(file, '.tbi'),
+                indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+    }
+  }]);
+  return BedPlugin;
+}(_Plugin2["default"]);
+
+exports["default"] = BedPlugin;

package/dist/index.test.js

@@ -0,0 +1,24 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+test('plugin in a stock JBrowse', function () {
+  console.warn = jest.fn();
+  var pluginManager = new _PluginManager["default"]([new _["default"]()]);
+  pluginManager.createPluggableElements();
+  pluginManager.configure();
+  expect(function () {
+    return pluginManager.addPlugin(new _["default"]());
+  }).toThrow(/JBrowse already configured, cannot add plugins/);
+  var BigBedAdapter = pluginManager.getAdapterType('BigBedAdapter');
+  var config = BigBedAdapter.configSchema.create({
+    type: 'BigBedAdapter'
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+});

package/dist/util.d.ts

@@ -1,2 +1,2 @@
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature';
-export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
+import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature';
+export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;

package/dist/util.js

@@ -0,0 +1,124 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.ucscProcessedTranscript = ucscProcessedTranscript;
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+function ucscProcessedTranscript(feature) {
+  var children = feature.children(); // split the blocks into UTR, CDS, and exons
+
+  var thickStart = feature.get('thickStart');
+  var thickEnd = feature.get('thickEnd');
+
+  if (!thickStart && !thickEnd) {
+    return feature;
+  }
+
+  var blocks = children ? children.filter(function (child) {
+    return child.get('type') === 'block';
+  }).sort(function (a, b) {
+    return a.get('start') - b.get('start');
+  }) : []; // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  var newChildren = [];
+  blocks.forEach(function (block) {
+    var start = block.get('start');
+    var end = block.get('end');
+
+    if (thickStart >= end) {
+      // left-side UTR
+      var prime = feature.get('strand') > 0 ? 'five' : 'three';
+      newChildren.push({
+        type: "".concat(prime, "_prime_UTR"),
+        start: start,
+        end: end
+      });
+    } else if (thickStart > start && thickStart < end && thickEnd >= end) {
+      // UTR | CDS
+      var _prime = feature.get('strand') > 0 ? 'five' : 'three';
+
+      newChildren.push({
+        type: "".concat(_prime, "_prime_UTR"),
+        start: start,
+        end: thickStart
+      }, {
+        type: 'CDS',
+        start: thickStart,
+        end: end
+      });
+    } else if (thickStart <= start && thickEnd >= end) {
+      // CDS
+      newChildren.push({
+        type: 'CDS',
+        start: start,
+        end: end
+      });
+    } else if (thickStart > start && thickStart < end && thickEnd < end) {
+      // UTR | CDS | UTR
+      var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
+      var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
+      newChildren.push({
+        type: "".concat(leftPrime, "_prime_UTR"),
+        start: start,
+        end: thickStart
+      }, {
+        type: "CDS",
+        start: thickStart,
+        end: thickEnd
+      }, {
+        type: "".concat(rightPrime, "_prime_UTR"),
+        start: thickEnd,
+        end: end
+      });
+    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+      // CDS | UTR
+      var _prime2 = feature.get('strand') > 0 ? 'three' : 'five';
+
+      newChildren.push({
+        type: "CDS",
+        start: start,
+        end: thickEnd
+      }, {
+        type: "".concat(_prime2, "_prime_UTR"),
+        start: thickEnd,
+        end: end
+      });
+    } else if (thickEnd <= start) {
+      // right-side UTR
+      var _prime3 = feature.get('strand') > 0 ? 'three' : 'five';
+
+      newChildren.push({
+        type: "".concat(_prime3, "_prime_UTR"),
+        start: start,
+        end: end
+      });
+    }
+  }); // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  var newData = {};
+  feature.tags().forEach(function (tag) {
+    newData[tag] = feature.get(tag);
+  });
+  newData.subfeatures = newChildren;
+  newData.type = 'mRNA';
+  newData.uniqueId = feature.id();
+  delete newData.chromStarts;
+  delete newData.chromStart;
+  delete newData.chromEnd;
+  delete newData.chrom;
+  delete newData.blockStarts;
+  delete newData.blockSizes;
+  delete newData.blockCount;
+  delete newData.thickStart;
+  delete newData.thickEnd;
+  var newFeature = new _simpleFeature["default"]({
+    data: newData,
+    id: feature.id()
+  });
+  return newFeature;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "1.6.8",
+  "version": "1.7.1",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-bed.esm.js",
-  "module": "dist/plugin-bed.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/bed",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@gmod/bbi": "^1.0.32",
@@ -47,5 +45,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "585e522096651ef4afb188366bb46d723439dc1b"
+  "gitHead": "6da232090c90f22ac96fd464c33082c89b8da14b"
 }

package/dist/index.test.d.ts

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