@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -0,0 +1 @@
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package/dist/CramAdapter/CramTestAdapters.js

@@ -1,234 +1,176 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.SequenceAdapter = exports.FetchableSmallFasta = void 0;
-exports.parseSmallFasta = parseSmallFasta;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-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 _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _toArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toArray"));
-
-var _rxjs = require("rxjs");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _configurationSchema = require("@jbrowse/core/configuration/configurationSchema");
-
-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 __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 });
+exports.SequenceAdapter = exports.FetchableSmallFasta = exports.parseSmallFasta = void 0;
+var rxjs_1 = require("rxjs");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var configurationSchema_1 = require("@jbrowse/core/configuration/configurationSchema");
 // setup for Cram Adapter Testing
 function parseSmallFasta(text) {
-  return text.split('>').filter(function (t) {
-    return /\S/.test(t);
-  }).map(function (entryText) {
-    var _entryText$split = entryText.split('\n'),
-        _entryText$split2 = (0, _toArray2.default)(_entryText$split),
-        defLine = _entryText$split2[0],
-        seqLines = _entryText$split2.slice(1);
-
-    var _defLine$split = defLine.split(' '),
-        _defLine$split2 = (0, _toArray2.default)(_defLine$split),
-        id = _defLine$split2[0],
-        descriptionLines = _defLine$split2.slice(1);
-
-    var description = descriptionLines.join(' ');
-    var sequence = seqLines.join('').replace(/\s/g, '');
-    return {
-      id: id,
-      description: description,
-      sequence: sequence
-    };
-  });
-}
-
-var FetchableSmallFasta = /*#__PURE__*/function () {
-  function FetchableSmallFasta(filehandle) {
-    (0, _classCallCheck2.default)(this, FetchableSmallFasta);
-    (0, _defineProperty2.default)(this, "data", void 0);
-    this.data = filehandle.readFile().then(function (buffer) {
-      var text = buffer.toString('utf8');
-      return parseSmallFasta(text);
+    return text
+        .split('>')
+        .filter(function (t) { return /\S/.test(t); })
+        .map(function (entryText) {
+        var _a = __read(entryText.split('\n')), defLine = _a[0], seqLines = _a.slice(1);
+        var _b = __read(defLine.split(' ')), id = _b[0], descriptionLines = _b.slice(1);
+        var description = descriptionLines.join(' ');
+        var sequence = seqLines.join('').replace(/\s/g, '');
+        return { id: id, description: description, sequence: sequence };
     });
-  }
-
-  (0, _createClass2.default)(FetchableSmallFasta, [{
-    key: "fetch",
-    value: function () {
-      var _fetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(id, start, end) {
-        var data, entry, length;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.data;
-
-              case 2:
-                data = _context.sent;
-                entry = data[id];
-                length = end - start + 1;
-
-                if (entry) {
-                  _context.next = 7;
-                  break;
+}
+exports.parseSmallFasta = parseSmallFasta;
+var FetchableSmallFasta = /** @class */ (function () {
+    function FetchableSmallFasta(filehandle) {
+        this.data = filehandle.readFile().then(function (buffer) {
+            var text = buffer.toString('utf8');
+            return parseSmallFasta(text);
+        });
+    }
+    FetchableSmallFasta.prototype.fetch = function (id, start, end) {
+        return __awaiter(this, void 0, void 0, function () {
+            var data, entry, length;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.data];
+                    case 1:
+                        data = _a.sent();
+                        entry = data[id];
+                        length = end - start + 1;
+                        if (!entry) {
+                            throw new Error("no sequence with id ".concat(id, " exists"));
+                        }
+                        return [2 /*return*/, entry.sequence.substr(start - 1, length)];
                 }
-
-                throw new Error("no sequence with id ".concat(id, " exists"));
-
-              case 7:
-                return _context.abrupt("return", entry.sequence.substr(start - 1, length));
-
-              case 8:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function fetch(_x, _x2, _x3) {
-        return _fetch.apply(this, arguments);
-      }
-
-      return fetch;
-    }()
-  }, {
-    key: "getSequenceList",
-    value: function () {
-      var _getSequenceList = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var data;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.data;
-
-              case 2:
-                data = _context2.sent;
-                return _context2.abrupt("return", data.map(function (entry) {
-                  return entry.id;
-                }));
-
-              case 4:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getSequenceList() {
-        return _getSequenceList.apply(this, arguments);
-      }
-
-      return getSequenceList;
-    }()
-  }]);
-  return FetchableSmallFasta;
-}();
-
-exports.FetchableSmallFasta = FetchableSmallFasta;
-
-var SequenceAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(SequenceAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(SequenceAdapter);
-
-  function SequenceAdapter(filehandle) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, SequenceAdapter);
-    _this = _super.call(this, (0, _configurationSchema.ConfigurationSchema)('empty', {}).create());
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "fasta", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "refNames", []);
-    _this.fasta = new FetchableSmallFasta(filehandle);
-    return _this;
-  }
-
-  (0, _createClass2.default)(SequenceAdapter, [{
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                return _context3.abrupt("return", this.refNames);
-
-              case 1:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(_ref) {
-      var _this2 = this;
-
-      var refName = _ref.refName,
-          start = _ref.start,
-          end = _ref.end;
-      return new _rxjs.Observable(function (observer) {
-        _this2.fasta.getSequenceList().then(function (refNames) {
-          _this2.refNames = refNames;
-        }).then(function () {
-          return _this2.fasta.fetch(_this2.refNames.indexOf(refName), start, end);
-        }).then(function (ret) {
-          observer.next(new _simpleFeature.default({
-            uniqueId: "".concat(refName, "-").concat(start, "-").concat(end),
-            seq: ret,
-            start: start,
-            end: end
-          }));
-          observer.complete();
+            });
+        });
+    };
+    FetchableSmallFasta.prototype.getSequenceList = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var data;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.data];
+                    case 1:
+                        data = _a.sent();
+                        return [2 /*return*/, data.map(function (entry) { return entry.id; })];
+                }
+            });
         });
-
-        return {
-          unsubscribe: function unsubscribe() {}
-        };
-      });
+    };
+    return FetchableSmallFasta;
+}());
+exports.FetchableSmallFasta = FetchableSmallFasta;
+var SequenceAdapter = /** @class */ (function (_super) {
+    __extends(SequenceAdapter, _super);
+    function SequenceAdapter(filehandle) {
+        var _this = _super.call(this, (0, configurationSchema_1.ConfigurationSchema)('empty', {}).create()) || this;
+        _this.refNames = [];
+        _this.fasta = new FetchableSmallFasta(filehandle);
+        return _this;
     }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return SequenceAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.SequenceAdapter = SequenceAdapter;
+    SequenceAdapter.prototype.getRefNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this.refNames];
+            });
+        });
+    };
+    SequenceAdapter.prototype.getFeatures = function (_a) {
+        var _this = this;
+        var refName = _a.refName, start = _a.start, end = _a.end;
+        return new rxjs_1.Observable(function (observer) {
+            _this.fasta
+                .getSequenceList()
+                .then(function (refNames) {
+                _this.refNames = refNames;
+            })
+                .then(function () {
+                return _this.fasta.fetch(_this.refNames.indexOf(refName), start, end);
+            })
+                .then(function (ret) {
+                observer.next(new simpleFeature_1.default({
+                    uniqueId: "".concat(refName, "-").concat(start, "-").concat(end),
+                    seq: ret,
+                    start: start,
+                    end: end,
+                }));
+                observer.complete();
+            });
+            return { unsubscribe: function () { } };
+        });
+    };
+    SequenceAdapter.prototype.freeResources = function ( /* { region } */) { };
+    return SequenceAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.SequenceAdapter = SequenceAdapter;
+//# sourceMappingURL=CramTestAdapters.js.map

package/dist/CramAdapter/CramTestAdapters.js.map

@@ -0,0 +1 @@
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package/dist/CramAdapter/configSchema.js

@@ -1,40 +1,30 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _default = function _default(pluginManager) {
-  return _mobxStateTree.types.late(function () {
-    return (0, _configuration.ConfigurationSchema)('CramAdapter', {
-      fetchSizeLimit: {
-        type: 'number',
-        defaultValue: 3000000
-      },
-      cramLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.cram',
-          locationType: 'UriLocation'
-        }
-      },
-      craiLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.cram.crai',
-          locationType: 'UriLocation'
-        }
-      },
-      sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter')
-    }, {
-      explicitlyTyped: true
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (function (pluginManager) {
+    return mobx_state_tree_1.types.late(function () {
+        return (0, configuration_1.ConfigurationSchema)('CramAdapter', {
+            fetchSizeLimit: {
+                type: 'number',
+                defaultValue: 3000000,
+            },
+            cramLocation: {
+                type: 'fileLocation',
+                defaultValue: {
+                    uri: '/path/to/my.cram',
+                    locationType: 'UriLocation',
+                },
+            },
+            craiLocation: {
+                type: 'fileLocation',
+                defaultValue: {
+                    uri: '/path/to/my.cram.crai',
+                    locationType: 'UriLocation',
+                },
+            },
+            sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        }, { explicitlyTyped: true });
     });
-  });
-};
-
-exports.default = _default;
+});
+//# sourceMappingURL=configSchema.js.map

package/dist/CramAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/CramAdapter/index.js

@@ -1,36 +1,41 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-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 || (0, _typeof2.default)(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; }
-
-var _default = function _default(pluginManager) {
-  pluginManager.addAdapterType(function () {
-    return new _AdapterType.default({
-      name: 'CramAdapter',
-      configSchema: pluginManager.load(_configSchema.default),
-      getAdapterClass: function getAdapterClass() {
-        return Promise.resolve().then(function () {
-          return _interopRequireWildcard(require('./CramAdapter'));
-        }).then(function (r) {
-          return r.default;
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+// locals
+var configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (function (pluginManager) {
+    pluginManager.addAdapterType(function () {
+        return new AdapterType_1.default({
+            name: 'CramAdapter',
+            configSchema: pluginManager.load(configSchema_1.default),
+            getAdapterClass: function () { return Promise.resolve().then(function () { return __importStar(require('./CramAdapter')); }).then(function (r) { return r.default; }); },
         });
-      }
     });
-  });
-};
-
-exports.default = _default;
+});
+//# sourceMappingURL=index.js.map

package/dist/CramAdapter/index.js.map

@@ -0,0 +1 @@
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