@jbrowse/plugin-bed 1.7.9 → 2.0.0

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -1,295 +1,160 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-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 _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 _bed = _interopRequireDefault(require("@gmod/bed"));
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _tabix = require("@gmod/tabix");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _util = 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; }
-
-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 BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(BedTabixAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(BedTabixAdapter);
-
-  function BedTabixAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BedTabixAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "parser", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bed", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "columnNames", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "scoreColumn", void 0);
-    var bedGzLocation = (0, _configuration.readConfObject)(config, 'bedGzLocation');
-    var index = (0, _configuration.readConfObject)(config, 'index');
-    var autoSql = (0, _configuration.readConfObject)(config, 'autoSql');
-    var location = index.location,
-        indexType = index.indexType;
-    _this.bed = new _tabix.TabixIndexedFile({
-      filehandle: (0, _io.openLocation)(bedGzLocation, _this.pluginManager),
-      csiFilehandle: indexType === 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
-      tbiFilehandle: indexType !== 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
-      chunkCacheSize: 50 * Math.pow(2, 20)
+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());
     });
-    _this.columnNames = (0, _configuration.readConfObject)(config, 'columnNames');
-    _this.scoreColumn = (0, _configuration.readConfObject)(config, 'scoreColumn');
-    _this.parser = new _bed.default({
-      autoSql: autoSql
-    });
-    return _this;
-  }
-
-  (0, _createClass2.default)(BedTabixAdapter, [{
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var opts,
-            _args = arguments;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-                return _context.abrupt("return", this.bed.getReferenceSequenceNames(opts));
-
-              case 2:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                return _context2.abrupt("return", this.bed.getHeader());
-
-              case 1:
-              case "end":
-                return _context2.stop();
+};
+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;
             }
-          }
-        }, _callee2, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "defaultParser",
-    value: function defaultParser(fields, line) {
-      return Object.fromEntries(line.split('\t').map(function (f, i) {
-        return [fields[i], f];
-      }));
+            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 };
     }
-  }, {
-    key: "getNames",
-    value: function () {
-      var _getNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var header, defs, defline;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                if (!this.columnNames.length) {
-                  _context3.next = 2;
-                  break;
-                }
-
-                return _context3.abrupt("return", this.columnNames);
-
-              case 2:
-                _context3.next = 4;
-                return this.bed.getHeader();
-
-              case 4:
-                header = _context3.sent;
-                defs = header.split('\n').filter(function (f) {
-                  return !!f;
-                });
-                defline = defs[defs.length - 1];
-                return _context3.abrupt("return", defline && defline.includes('\t') ? defline.slice(1).split('\t').map(function (field) {
-                  return field.trim();
-                }) : null);
-
-              case 8:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getNames() {
-        return _getNames.apply(this, arguments);
-      }
-
-      return getNames;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query) {
-      var _this2 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
-          var meta, columnNumbers, colRef, colStart, colEnd, colSame, names;
-          return _regenerator.default.wrap(function _callee4$(_context4) {
-            while (1) {
-              switch (_context4.prev = _context4.next) {
-                case 0:
-                  _context4.next = 2;
-                  return _this2.bed.getMetadata();
-
-                case 2:
-                  meta = _context4.sent;
-                  columnNumbers = meta.columnNumbers;
-                  colRef = columnNumbers.ref - 1;
-                  colStart = columnNumbers.start - 1;
-                  colEnd = columnNumbers.end - 1; // colSame handles special case for tabix where a single column is both
-                  // the start and end, this is assumed to be covering the base at this
-                  // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
-
-                  colSame = colStart === colEnd ? 1 : 0;
-                  _context4.next = 10;
-                  return _this2.getNames();
-
-                case 10:
-                  names = _context4.sent;
-                  _context4.next = 13;
-                  return _this2.bed.getLines(query.refName, query.start, query.end, {
-                    lineCallback: function lineCallback(line, fileOffset) {
-                      var l = line.split('\t');
-                      var refName = l[colRef];
-                      var start = +l[colStart];
-                      var end = +l[colEnd] + colSame;
-                      var uniqueId = "".concat(_this2.id, "-").concat(fileOffset);
-                      var data = names ? _this2.defaultParser(names, line) : _this2.parser.parseLine(line, {
-                        uniqueId: uniqueId
-                      });
-                      var blockCount = data.blockCount,
-                          blockSizes = data.blockSizes,
-                          blockStarts = data.blockStarts,
-                          chromStarts = data.chromStarts;
-
-                      if (blockCount) {
-                        var starts = chromStarts || blockStarts || [];
-                        var sizes = blockSizes;
-                        var blocksOffset = start;
-                        data.subfeatures = [];
-
-                        for (var b = 0; b < blockCount; b += 1) {
-                          var bmin = (starts[b] || 0) + blocksOffset;
-                          var bmax = bmin + (sizes[b] || 0);
-                          data.subfeatures.push({
-                            uniqueId: "".concat(uniqueId, "-").concat(b),
-                            start: bmin,
-                            end: bmax,
-                            type: 'block'
-                          });
-                        }
-                      }
-
-                      if (_this2.scoreColumn) {
-                        data.score = +data[_this2.scoreColumn];
-                      }
-
-                      delete data.chrom;
-                      delete data.chromStart;
-                      delete data.chromEnd;
-                      var f = new _simpleFeature.default(_objectSpread(_objectSpread({}, data), {}, {
-                        start: start,
-                        end: end,
-                        refName: refName,
-                        uniqueId: uniqueId
-                      }));
-                      var r = f.get('thickStart') ? (0, _util.ucscProcessedTranscript)(f) : f;
-                      observer.next(r);
-                    },
-                    signal: opts.signal
-                  });
-
-                case 13:
-                  observer.complete();
-
-                case 14:
-                case "end":
-                  return _context4.stop();
-              }
-            }
-          }, _callee4);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+var bed_1 = __importDefault(require("@gmod/bed"));
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var tabix_1 = require("@gmod/tabix");
+var util_1 = require("../util");
+var BedTabixAdapter = /** @class */ (function (_super) {
+    __extends(BedTabixAdapter, _super);
+    function BedTabixAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var bedGzLoc = _this.getConf('bedGzLocation');
+        var type = _this.getConf(['index', 'indexType']);
+        var loc = _this.getConf(['index', 'location']);
+        var autoSql = _this.getConf('autoSql');
+        var pm = _this.pluginManager;
+        _this.bed = new tabix_1.TabixIndexedFile({
+            filehandle: (0, io_1.openLocation)(bedGzLoc, pm),
+            csiFilehandle: type === 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
+            tbiFilehandle: type !== 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
+            chunkCacheSize: 50 * Math.pow(2, 20),
+        });
+        _this.columnNames = _this.getConf('columnNames');
+        _this.scoreColumn = _this.getConf('scoreColumn');
+        _this.parser = new bed_1.default({ autoSql: autoSql });
+        return _this;
     }
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return BedTabixAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
+    BedTabixAdapter.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this.bed.getReferenceSequenceNames(opts)];
+            });
+        });
+    };
+    BedTabixAdapter.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this.bed.getHeader()];
+            });
+        });
+    };
+    BedTabixAdapter.prototype.getNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header, defs, defline;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        if (this.columnNames.length) {
+                            return [2 /*return*/, this.columnNames];
+                        }
+                        return [4 /*yield*/, this.bed.getHeader()];
+                    case 1:
+                        header = _a.sent();
+                        defs = header.split('\n').filter(function (f) { return !!f; });
+                        defline = defs[defs.length - 1];
+                        return [2 /*return*/, (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+                                ? defline
+                                    .slice(1)
+                                    .split('\t')
+                                    .map(function (f) { return f.trim(); })
+                                : undefined];
+                }
+            });
+        });
+    };
+    BedTabixAdapter.prototype.getFeatures = function (query, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var meta, columnNumbers, colRef, colStart, colEnd, names;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.bed.getMetadata()];
+                    case 1:
+                        meta = _a.sent();
+                        columnNumbers = meta.columnNumbers;
+                        colRef = columnNumbers.ref - 1;
+                        colStart = columnNumbers.start - 1;
+                        colEnd = columnNumbers.end - 1;
+                        return [4 /*yield*/, this.getNames()];
+                    case 2:
+                        names = _a.sent();
+                        return [4 /*yield*/, this.bed.getLines(query.refName, query.start, query.end, {
+                                lineCallback: function (line, fileOffset) {
+                                    observer.next((0, util_1.featureData)(line, colRef, colStart, colEnd, _this.scoreColumn, _this.parser, "".concat(_this.id, "-").concat(fileOffset), names));
+                                },
+                                signal: opts.signal,
+                            })];
+                    case 3:
+                        _a.sent();
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    BedTabixAdapter.prototype.freeResources = function () { };
+    BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
+    return BedTabixAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
 exports.default = BedTabixAdapter;
-(0, _defineProperty2.default)(BedTabixAdapter, "capabilities", ['getFeatures', 'getRefNames']);
+//# sourceMappingURL=BedTabixAdapter.js.map

package/dist/BedTabixAdapter/BedTabixAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,kDAA2B;AAC3B,uEAGgD;AAChD,4CAAoD;AACpD,gDAA0D;AAE1D,qCAA8C;AAC9C,gCAAqC;AAKrC;IAA6C,mCAAsB;IAWjE,yBACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAH/B,YAKE,kBAAM,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,SAgB5C;QAfC,IAAM,QAAQ,GAAG,KAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,IAAM,IAAI,GAAG,KAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,IAAM,GAAG,GAAG,KAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,IAAM,OAAO,GAAG,KAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,IAAM,EAAE,GAAG,KAAI,CAAC,aAAa,CAAA;QAE7B,KAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA;SAC7B,CAAC,CAAA;QACF,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,KAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,SAAA,EAAE,CAAC,CAAA;;IACpC,CAAC;IAEY,qCAAW,GAAxB,UAAyB,IAAsB;QAAtB,qBAAA,EAAA,SAAsB;;;gBAC7C,sBAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,EAAA;;;KAChD;IAEK,mCAAS,GAAf;;;gBACE,sBAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,EAAA;;;KAC5B;IAEK,kCAAQ,GAAd;;;;;;wBACE,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;4BAC3B,sBAAO,IAAI,CAAC,WAAW,EAAA;yBACxB;wBACc,qBAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,EAAA;;wBAAnC,MAAM,GAAG,SAA0B;wBACnC,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;wBAC1C,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;wBACrC,sBAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;gCAC5B,CAAC,CAAC,OAAO;qCACJ,KAAK,CAAC,CAAC,CAAC;qCACR,KAAK,CAAC,IAAI,CAAC;qCACX,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,IAAI,EAAE,EAAR,CAAQ,CAAC;gCACvB,CAAC,CAAC,SAAS,EAAA;;;;KACd;IAEM,qCAAW,GAAlB,UAAmB,KAAa,EAAE,IAAsB;QAAxD,iBA8BC;QA9BiC,qBAAA,EAAA,SAAsB;QACtD,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;;;4BAChC,qBAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,EAAA;;wBAAnC,IAAI,GAAG,SAA4B;wBACjC,aAAa,GAAK,IAAI,cAAT,CAAS;wBACxB,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;wBAC9B,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;wBAClC,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;wBAItB,qBAAM,IAAI,CAAC,QAAQ,EAAE,EAAA;;wBAA7B,KAAK,GAAG,SAAqB;wBACnC,qBAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gCAC7D,YAAY,EAAE,UAAC,IAAI,EAAE,UAAU;oCAC7B,QAAQ,CAAC,IAAI,CACX,IAAA,kBAAW,EACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,KAAI,CAAC,WAAW,EAChB,KAAI,CAAC,MAAM,EACX,UAAG,KAAI,CAAC,EAAE,cAAI,UAAU,CAAE,EAC1B,KAAK,CACN,CACF,CAAA;gCACH,CAAC;gCACD,MAAM,EAAE,IAAI,CAAC,MAAM;6BACpB,CAAC,EAAA;;wBAhBF,SAgBE,CAAA;wBACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;;aACpB,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,uCAAa,GAApB,cAA8B,CAAC;IAhFjB,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;IAiF7D,sBAAC;CAAA,AA1FD,CAA6C,oCAAsB,GA0FlE;kBA1FoB,eAAe"}

package/dist/BedTabixAdapter/configSchema.js

@@ -1,53 +1,40 @@
 "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 = (0, _configuration.ConfigurationSchema)('BedTabixAdapter', {
-  bedGzLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.bed.gz',
-      locationType: 'UriLocation'
-    }
-  },
-  index: (0, _configuration.ConfigurationSchema)('TabixIndex', {
-    indexType: {
-      model: _mobxStateTree.types.enumeration('IndexType', ['TBI', 'CSI']),
-      type: 'stringEnum',
-      defaultValue: 'TBI'
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_state_tree_1 = require("mobx-state-tree");
+exports.default = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
+    bedGzLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
-    location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my.bed.gz.tbi',
-        locationType: 'UriLocation'
-      }
-    }
-  }),
-  columnNames: {
-    type: 'stringArray',
-    description: 'List of column names',
-    defaultValue: []
-  },
-  scoreColumn: {
-    type: 'string',
-    description: 'The column to use as a "score" attribute',
-    defaultValue: ''
-  },
-  autoSql: {
-    type: 'string',
-    description: 'The autoSql definition for the data fields in the file',
-    defaultValue: ''
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+    index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
+        indexType: {
+            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.bed.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+    scoreColumn: {
+        type: 'string',
+        description: 'The column to use as a "score" attribute',
+        defaultValue: '',
+    },
+    autoSql: {
+        type: 'string',
+        description: 'The autoSql definition for the data fields in the file',
+        defaultValue: '',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/BedTabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,mDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,KAAK,EAAE,IAAA,mCAAmB,EAAC,YAAY,EAAE;QACvC,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IAEF,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BedTabixAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/BedTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}