@jbrowse/plugin-gff3 1.7.9 → 2.0.0

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -1,395 +1,314 @@
 "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 _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _range = require("@jbrowse/core/util/range");
-
-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 _gff = _interopRequireDefault(require("@gmod/gff"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-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 _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(_default, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(_default);
-
-  function _default(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "gff", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "dontRedispatch", void 0);
-    var gffGzLocation = (0, _configuration.readConfObject)(config, 'gffGzLocation');
-    var indexType = (0, _configuration.readConfObject)(config, ['index', 'indexType']);
-    var location = (0, _configuration.readConfObject)(config, ['index', 'location']);
-    var dontRedispatch = (0, _configuration.readConfObject)(config, 'dontRedispatch');
-    _this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
-    _this.gff = new _tabix.TabixIndexedFile({
-      filehandle: (0, _io.openLocation)(gffGzLocation, _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),
-      renameRefSeqs: function renameRefSeqs(n) {
-        return n;
-      }
+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 __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __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());
     });
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    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$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-                return _context.abrupt("return", this.gff.getReferenceSequenceNames(opts));
-
-              case 2:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                return _context2.abrupt("return", this.gff.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: "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 _callee3(observer) {
-          var metadata;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  _context3.next = 2;
-                  return _this2.gff.getMetadata();
-
-                case 2:
-                  metadata = _context3.sent;
-
-                  _this2.getFeaturesHelper(query, opts, metadata, observer, true);
-
-                case 4:
-                case "end":
-                  return _context3.stop();
-              }
-            }
-          }, _callee3);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
-  }, {
-    key: "getFeaturesHelper",
-    value: function () {
-      var _getFeaturesHelper = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(query) {
-        var _this3 = this;
-
-        var opts,
-            metadata,
-            observer,
-            allowRedispatch,
-            originalQuery,
-            lines,
-            minStart,
-            maxEnd,
-            gff3,
-            features,
-            _args4 = arguments;
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                opts = _args4.length > 1 && _args4[1] !== undefined ? _args4[1] : {};
-                metadata = _args4.length > 2 ? _args4[2] : undefined;
-                observer = _args4.length > 3 ? _args4[3] : undefined;
-                allowRedispatch = _args4.length > 4 ? _args4[4] : undefined;
-                originalQuery = _args4.length > 5 && _args4[5] !== undefined ? _args4[5] : query;
-                _context4.prev = 5;
-                lines = [];
-                _context4.next = 9;
-                return this.gff.getLines(query.refName, query.start, query.end, function (line, fileOffset) {
-                  lines.push(_this3.parseLine(metadata.columnNumbers, line, fileOffset));
-                });
-
-              case 9:
-                if (!(allowRedispatch && lines.length)) {
-                  _context4.next = 16;
-                  break;
-                }
-
-                minStart = Infinity;
-                maxEnd = -Infinity;
-                lines.forEach(function (line) {
-                  var featureType = line.fields[2]; // only expand redispatch range if feature is not a "dontRedispatch" type
-                  // skips large regions like chromosome,region
-
-                  if (!_this3.dontRedispatch.includes(featureType)) {
-                    var start = line.start - 1; // gff is 1-based
-
-                    if (start < minStart) {
-                      minStart = start;
-                    }
-
-                    if (line.end > maxEnd) {
-                      maxEnd = line.end;
-                    }
-                  }
-                });
-
-                if (!(maxEnd > query.end || minStart < query.start)) {
-                  _context4.next = 16;
-                  break;
-                }
-
-                // make a new feature callback to only return top-level features
-                // in the original query range
-                this.getFeaturesHelper(_objectSpread(_objectSpread({}, query), {}, {
-                  start: minStart,
-                  end: maxEnd
-                }), opts, metadata, observer, false, query);
-                return _context4.abrupt("return");
-
-              case 16:
-                gff3 = lines.map(function (lineRecord) {
-                  if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
-                    if (!lineRecord.fields[8].includes('_lineHash')) {
-                      lineRecord.fields[8] += ";_lineHash=".concat(lineRecord.lineHash);
-                    }
-                  } else {
-                    lineRecord.fields[8] = "_lineHash=".concat(lineRecord.lineHash);
-                  }
-
-                  return lineRecord.fields.join('\t');
-                }).join('\n');
-                features = _gff.default.parseStringSync(gff3, {
-                  parseFeatures: true,
-                  parseComments: false,
-                  parseDirectives: false,
-                  parseSequences: false
-                });
-                features.forEach(function (featureLocs) {
-                  return _this3.formatFeatures(featureLocs).forEach(function (f) {
-                    if ((0, _range.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
-                      observer.next(f);
-                    }
-                  });
-                });
-                observer.complete();
-                _context4.next = 25;
-                break;
-
-              case 22:
-                _context4.prev = 22;
-                _context4.t0 = _context4["catch"](5);
-                observer.error(_context4.t0);
-
-              case 25:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this, [[5, 22]]);
-      }));
-
-      function getFeaturesHelper(_x2) {
-        return _getFeaturesHelper.apply(this, arguments);
-      }
-
-      return getFeaturesHelper;
-    }()
-  }, {
-    key: "parseLine",
-    value: function parseLine(columnNumbers, line, fileOffset) {
-      var fields = line.split('\t'); // note: index column numbers are 1-based
-
-      return {
-        start: +fields[columnNumbers.start - 1],
-        end: +fields[columnNumbers.end - 1],
-        lineHash: fileOffset,
-        fields: fields
-      };
+};
+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);
     }
-  }, {
-    key: "formatFeatures",
-    value: function formatFeatures(featureLocs) {
-      var _this4 = this;
-
-      return featureLocs.map(function (featureLoc) {
-        return new _simpleFeature.default({
-          data: _this4.featureData(featureLoc),
-          // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-          id: "".concat(_this4.id, "-offset-").concat(featureLoc.attributes._lineHash[0])
+    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 });
+/* eslint-disable no-underscore-dangle */
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var range_1 = require("@jbrowse/core/util/range");
+var io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var tabix_1 = require("@gmod/tabix");
+var gff_1 = __importDefault(require("@gmod/gff"));
+var configuration_1 = require("@jbrowse/core/configuration");
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var gffGzLocation = (0, configuration_1.readConfObject)(config, 'gffGzLocation');
+        var indexType = (0, configuration_1.readConfObject)(config, ['index', 'indexType']);
+        var location = (0, configuration_1.readConfObject)(config, ['index', 'location']);
+        var dontRedispatch = (0, configuration_1.readConfObject)(config, 'dontRedispatch');
+        _this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
+        _this.gff = new tabix_1.TabixIndexedFile({
+            filehandle: (0, io_1.openLocation)(gffGzLocation, _this.pluginManager),
+            csiFilehandle: indexType === 'CSI'
+                ? (0, io_1.openLocation)(location, _this.pluginManager)
+                : undefined,
+            tbiFilehandle: indexType !== 'CSI'
+                ? (0, io_1.openLocation)(location, _this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * Math.pow(2, 20),
+            renameRefSeqs: function (n) { return n; },
         });
-      });
+        return _this;
     }
-  }, {
-    key: "featureData",
-    value: function featureData(data) {
-      var _this5 = this;
-
-      var f = _objectSpread({}, data);
-
-      f.start -= 1; // convert to interbase
-
-      if (data.strand === '+') {
-        f.strand = 1;
-      } else if (data.strand === '-') {
-        f.strand = -1;
-      } else if (data.strand === '.') {
-        f.strand = 0;
-      } else {
-        f.strand = undefined;
-      }
-
-      f.phase = Number(data.phase);
-      f.refName = data.seq_id;
-
-      if (data.score === null) {
-        delete f.score;
-      }
-
-      if (data.phase === null) {
-        delete f.score;
-      }
-
-      var defaultFields = ['start', 'end', 'seq_id', 'score', 'type', 'source', 'phase', 'strand'];
-      var dataAttributes = data.attributes || {};
-      Object.keys(dataAttributes).forEach(function (a) {
-        var b = a.toLowerCase();
-
-        if (defaultFields.includes(b)) {
-          // add "suffix" to tag name if it already exists
-          // reproduces behavior of NCList
-          b += '2';
+    default_1.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.gff.getReferenceSequenceNames(opts)];
+            });
+        });
+    };
+    default_1.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this.gff.getHeader()];
+            });
+        });
+    };
+    default_1.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 metadata;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.gff.getMetadata()];
+                    case 1:
+                        metadata = _a.sent();
+                        this.getFeaturesHelper(query, opts, metadata, observer, true);
+                        return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    default_1.prototype.getFeaturesHelper = function (query, opts, metadata, observer, allowRedispatch, originalQuery) {
+        if (opts === void 0) { opts = {}; }
+        if (originalQuery === void 0) { originalQuery = query; }
+        return __awaiter(this, void 0, void 0, function () {
+            var lines_1, minStart_1, maxEnd_1, gff3, features, e_1;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        _a.trys.push([0, 2, , 3]);
+                        lines_1 = [];
+                        return [4 /*yield*/, this.gff.getLines(query.refName, query.start, query.end, function (line, fileOffset) {
+                                lines_1.push(_this.parseLine(metadata.columnNumbers, line, fileOffset));
+                            })];
+                    case 1:
+                        _a.sent();
+                        if (allowRedispatch && lines_1.length) {
+                            minStart_1 = Infinity;
+                            maxEnd_1 = -Infinity;
+                            lines_1.forEach(function (line) {
+                                var featureType = line.fields[2];
+                                // only expand redispatch range if feature is not a "dontRedispatch" type
+                                // skips large regions like chromosome,region
+                                if (!_this.dontRedispatch.includes(featureType)) {
+                                    var start = line.start - 1; // gff is 1-based
+                                    if (start < minStart_1) {
+                                        minStart_1 = start;
+                                    }
+                                    if (line.end > maxEnd_1) {
+                                        maxEnd_1 = line.end;
+                                    }
+                                }
+                            });
+                            if (maxEnd_1 > query.end || minStart_1 < query.start) {
+                                // make a new feature callback to only return top-level features
+                                // in the original query range
+                                this.getFeaturesHelper(__assign(__assign({}, query), { start: minStart_1, end: maxEnd_1 }), opts, metadata, observer, false, query);
+                                return [2 /*return*/];
+                            }
+                        }
+                        gff3 = lines_1
+                            .map(function (lineRecord) {
+                            if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
+                                if (!lineRecord.fields[8].includes('_lineHash')) {
+                                    lineRecord.fields[8] += ";_lineHash=".concat(lineRecord.lineHash);
+                                }
+                            }
+                            else {
+                                lineRecord.fields[8] = "_lineHash=".concat(lineRecord.lineHash);
+                            }
+                            return lineRecord.fields.join('\t');
+                        })
+                            .join('\n');
+                        features = gff_1.default.parseStringSync(gff3, {
+                            parseFeatures: true,
+                            parseComments: false,
+                            parseDirectives: false,
+                            parseSequences: false,
+                        });
+                        features.forEach(function (featureLocs) {
+                            return _this.formatFeatures(featureLocs).forEach(function (f) {
+                                if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
+                                    observer.next(f);
+                                }
+                            });
+                        });
+                        observer.complete();
+                        return [3 /*break*/, 3];
+                    case 2:
+                        e_1 = _a.sent();
+                        observer.error(e_1);
+                        return [3 /*break*/, 3];
+                    case 3: return [2 /*return*/];
+                }
+            });
+        });
+    };
+    default_1.prototype.parseLine = function (columnNumbers, line, fileOffset) {
+        var fields = line.split('\t');
+        // note: index column numbers are 1-based
+        return {
+            start: +fields[columnNumbers.start - 1],
+            end: +fields[columnNumbers.end - 1],
+            lineHash: fileOffset,
+            fields: fields,
+        };
+    };
+    default_1.prototype.formatFeatures = function (featureLocs) {
+        var _this = this;
+        return featureLocs.map(function (featureLoc) {
+            return new simpleFeature_1.default({
+                data: _this.featureData(featureLoc),
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                id: "".concat(_this.id, "-offset-").concat(featureLoc.attributes._lineHash[0]),
+            });
+        });
+    };
+    default_1.prototype.featureData = function (data) {
+        var _this = this;
+        var f = __assign({}, data);
+        f.start -= 1; // convert to interbase
+        if (data.strand === '+') {
+            f.strand = 1;
         }
-
-        if (dataAttributes[a] !== null) {
-          var attr = dataAttributes[a];
-
-          if (Array.isArray(attr) && attr.length === 1) {
-            ;
-            var _attr = attr;
-
-            var _attr2 = (0, _slicedToArray2.default)(_attr, 1);
-
-            attr = _attr2[0];
-          }
-
-          f[b] = attr;
+        else if (data.strand === '-') {
+            f.strand = -1;
         }
-      });
-      f.refName = f.seq_id; // the SimpleFeature constructor takes care of recursively inflating subfeatures
-
-      if (data.child_features && data.child_features.length) {
-        f.subfeatures = data.child_features.map(function (childLocs) {
-          return childLocs.map(function (childLoc) {
-            return _this5.featureData(childLoc);
-          });
-        }).flat();
-      }
-
-      delete f.child_features;
-      delete f.data;
-      delete f.derived_features;
-      delete f._linehash;
-      delete f.attributes;
-      delete f.seq_id;
-      return f;
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = _default;
+        else if (data.strand === '.') {
+            f.strand = 0;
+        }
+        else {
+            f.strand = undefined;
+        }
+        f.phase = Number(data.phase);
+        f.refName = data.seq_id;
+        if (data.score === null) {
+            delete f.score;
+        }
+        if (data.phase === null) {
+            delete f.score;
+        }
+        var defaultFields = [
+            'start',
+            'end',
+            'seq_id',
+            'score',
+            'type',
+            'source',
+            'phase',
+            'strand',
+        ];
+        var dataAttributes = data.attributes || {};
+        Object.keys(dataAttributes).forEach(function (a) {
+            var _a, _b;
+            var b = a.toLowerCase();
+            if (defaultFields.includes(b)) {
+                // add "suffix" to tag name if it already exists
+                // reproduces behavior of NCList
+                b += '2';
+            }
+            if (dataAttributes[a] !== null) {
+                var attr = dataAttributes[a];
+                if (Array.isArray(attr) && attr.length === 1) {
+                    ;
+                    _a = attr, _b = __read(_a, 1), attr = _b[0];
+                }
+                f[b] = attr;
+            }
+        });
+        f.refName = f.seq_id;
+        // the SimpleFeature constructor takes care of recursively inflating subfeatures
+        if (data.child_features && data.child_features.length) {
+            f.subfeatures = data.child_features
+                .map(function (childLocs) { return childLocs.map(function (childLoc) { return _this.featureData(childLoc); }); })
+                .flat();
+        }
+        delete f.child_features;
+        delete f.data;
+        delete f.derived_features;
+        delete f._linehash;
+        delete f.attributes;
+        delete f.seq_id;
+        return f;
+    };
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    return default_1;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = default_1;
+//# sourceMappingURL=Gff3TabixAdapter.js.map