@jbrowse/plugin-bed 1.7.10 → 1.7.11

package/dist/BedAdapter/BedAdapter.d.ts

@@ -0,0 +1,29 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: typeof BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
+    protected intervalTrees: {
+        [key: string]: Promise<IntervalTree | undefined> | undefined;
+    };
+    static capabilities: string[];
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureIntervalTreeHelper;
+    private loadFeatureIntervalTree;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/BedAdapter/BedAdapter.js

@@ -0,0 +1,498 @@
+"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 _util = require("../util");
+
+var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
+
+var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
+
+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; } }
+
+function isGzip(buf) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+
+var BedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2.default)(BedAdapter, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(BedAdapter);
+
+  function BedAdapter() {
+    var _this;
+
+    (0, _classCallCheck2.default)(this, BedAdapter);
+
+    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), "bedFeatures", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "intervalTrees", {});
+    return _this;
+  }
+
+  (0, _createClass2.default)(BedAdapter, [{
+    key: "loadDataP",
+    value: function () {
+      var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+        var opts,
+            pm,
+            bedLoc,
+            buf,
+            buffer,
+            data,
+            lines,
+            headerLines,
+            i,
+            header,
+            features,
+            line,
+            tab,
+            refName,
+            autoSql,
+            parser,
+            columnNames,
+            scoreColumn,
+            colRef,
+            colStart,
+            colEnd,
+            _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] : {};
+                pm = this.pluginManager;
+                bedLoc = this.getConf('bedLocation');
+                _context.next = 5;
+                return (0, _io.openLocation)(bedLoc, pm).readFile(opts);
+
+              case 5:
+                buf = _context.sent;
+
+                if (!isGzip(buf)) {
+                  _context.next = 12;
+                  break;
+                }
+
+                _context.next = 9;
+                return (0, _bgzfFilehandle.unzip)(buf);
+
+              case 9:
+                _context.t0 = _context.sent;
+                _context.next = 13;
+                break;
+
+              case 12:
+                _context.t0 = buf;
+
+              case 13:
+                buffer = _context.t0;
+
+                if (!(buffer.length > 536870888)) {
+                  _context.next = 16;
+                  break;
+                }
+
+                throw new Error('Data exceeds maximum string length (512MB)');
+
+              case 16:
+                data = new TextDecoder('utf8', {
+                  fatal: true
+                }).decode(buffer);
+                lines = data.split('\n').filter(function (f) {
+                  return !!f;
+                });
+                headerLines = [];
+                i = 0;
+
+                for (; i < lines.length && lines[i].startsWith('#'); i++) {
+                  headerLines.push(lines[i]);
+                }
+
+                header = headerLines.join('\n');
+                features = {};
+
+                for (; i < lines.length; i++) {
+                  line = lines[i];
+                  tab = line.indexOf('\t');
+                  refName = line.slice(0, tab);
+
+                  if (!features[refName]) {
+                    features[refName] = [];
+                  }
+
+                  features[refName].push(line);
+                }
+
+                autoSql = this.getConf('autoSql');
+                parser = new _bed.default({
+                  autoSql: autoSql
+                });
+                columnNames = this.getConf('columnNames');
+                scoreColumn = this.getConf('scoreColumn');
+                colRef = this.getConf('colRef');
+                colStart = this.getConf('colStart');
+                colEnd = this.getConf('colEnd');
+                return _context.abrupt("return", {
+                  header: header,
+                  features: features,
+                  parser: parser,
+                  columnNames: columnNames,
+                  scoreColumn: scoreColumn,
+                  colRef: colRef,
+                  colStart: colStart,
+                  colEnd: colEnd
+                });
+
+              case 32:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function loadDataP() {
+        return _loadDataP.apply(this, arguments);
+      }
+
+      return loadDataP;
+    }()
+  }, {
+    key: "loadData",
+    value: function () {
+      var _loadData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+        var _this2 = this;
+
+        var opts,
+            _args2 = arguments;
+        return _regenerator.default.wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                opts = _args2.length > 0 && _args2[0] !== undefined ? _args2[0] : {};
+
+                if (!this.bedFeatures) {
+                  this.bedFeatures = this.loadDataP(opts).catch(function (e) {
+                    _this2.bedFeatures = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context2.abrupt("return", this.bedFeatures);
+
+              case 3:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function loadData() {
+        return _loadData.apply(this, arguments);
+      }
+
+      return loadData;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+        var opts,
+            _yield$this$loadData,
+            features,
+            _args3 = arguments;
+
+        return _regenerator.default.wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
+                _context3.next = 3;
+                return this.loadData(opts);
+
+              case 3:
+                _yield$this$loadData = _context3.sent;
+                features = _yield$this$loadData.features;
+                return _context3.abrupt("return", Object.keys(features));
+
+              case 6:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+        var opts,
+            _yield$this$loadData2,
+            header,
+            _args4 = arguments;
+
+        return _regenerator.default.wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                opts = _args4.length > 0 && _args4[0] !== undefined ? _args4[0] : {};
+                _context4.next = 3;
+                return this.loadData(opts);
+
+              case 3:
+                _yield$this$loadData2 = _context4.sent;
+                header = _yield$this$loadData2.header;
+                return _context4.abrupt("return", header);
+
+              case 6:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "getNames",
+    value: function () {
+      var _getNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
+        var _yield$this$loadData3, header, columnNames, defs, defline;
+
+        return _regenerator.default.wrap(function _callee5$(_context5) {
+          while (1) {
+            switch (_context5.prev = _context5.next) {
+              case 0:
+                _context5.next = 2;
+                return this.loadData();
+
+              case 2:
+                _yield$this$loadData3 = _context5.sent;
+                header = _yield$this$loadData3.header;
+                columnNames = _yield$this$loadData3.columnNames;
+
+                if (!columnNames.length) {
+                  _context5.next = 7;
+                  break;
+                }
+
+                return _context5.abrupt("return", columnNames);
+
+              case 7:
+                defs = header.split('\n').filter(function (f) {
+                  return !!f;
+                });
+                defline = defs[defs.length - 1];
+                return _context5.abrupt("return", defline !== null && defline !== void 0 && defline.includes('\t') ? defline.slice(1).split('\t').map(function (field) {
+                  return field.trim();
+                }) : undefined);
+
+              case 10:
+              case "end":
+                return _context5.stop();
+            }
+          }
+        }, _callee5, this);
+      }));
+
+      function getNames() {
+        return _getNames.apply(this, arguments);
+      }
+
+      return getNames;
+    }()
+  }, {
+    key: "loadFeatureIntervalTreeHelper",
+    value: function () {
+      var _loadFeatureIntervalTreeHelper = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(refName) {
+        var _this3 = this;
+
+        var _yield$this$loadData4, colRef, colStart, colEnd, features, parser, scoreColumn, lines, names, intervalTree, ret, i, obj;
+
+        return _regenerator.default.wrap(function _callee6$(_context6) {
+          while (1) {
+            switch (_context6.prev = _context6.next) {
+              case 0:
+                _context6.next = 2;
+                return this.loadData();
+
+              case 2:
+                _yield$this$loadData4 = _context6.sent;
+                colRef = _yield$this$loadData4.colRef;
+                colStart = _yield$this$loadData4.colStart;
+                colEnd = _yield$this$loadData4.colEnd;
+                features = _yield$this$loadData4.features;
+                parser = _yield$this$loadData4.parser;
+                scoreColumn = _yield$this$loadData4.scoreColumn;
+                lines = features[refName];
+
+                if (lines) {
+                  _context6.next = 12;
+                  break;
+                }
+
+                return _context6.abrupt("return", undefined);
+
+              case 12:
+                _context6.next = 14;
+                return this.getNames();
+
+              case 14:
+                names = _context6.sent;
+                intervalTree = new _intervalTree.default();
+                ret = lines.map(function (f, i) {
+                  var uniqueId = "".concat(_this3.id, "-").concat(refName, "-").concat(i);
+                  return (0, _util.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+                });
+
+                for (i = 0; i < ret.length; i++) {
+                  obj = ret[i];
+                  intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+                }
+
+                return _context6.abrupt("return", intervalTree);
+
+              case 19:
+              case "end":
+                return _context6.stop();
+            }
+          }
+        }, _callee6, this);
+      }));
+
+      function loadFeatureIntervalTreeHelper(_x) {
+        return _loadFeatureIntervalTreeHelper.apply(this, arguments);
+      }
+
+      return loadFeatureIntervalTreeHelper;
+    }()
+  }, {
+    key: "loadFeatureIntervalTree",
+    value: function () {
+      var _loadFeatureIntervalTree = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(refName) {
+        var _this4 = this;
+
+        return _regenerator.default.wrap(function _callee7$(_context7) {
+          while (1) {
+            switch (_context7.prev = _context7.next) {
+              case 0:
+                if (!this.intervalTrees[refName]) {
+                  this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
+                    _this4.intervalTrees[refName] = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context7.abrupt("return", this.intervalTrees[refName]);
+
+              case 2:
+              case "end":
+                return _context7.stop();
+            }
+          }
+        }, _callee7, this);
+      }));
+
+      function loadFeatureIntervalTree(_x2) {
+        return _loadFeatureIntervalTree.apply(this, arguments);
+      }
+
+      return loadFeatureIntervalTree;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this5 = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(observer) {
+          var start, end, refName, intervalTree;
+          return _regenerator.default.wrap(function _callee8$(_context8) {
+            while (1) {
+              switch (_context8.prev = _context8.next) {
+                case 0:
+                  start = query.start, end = query.end, refName = query.refName;
+                  _context8.next = 3;
+                  return _this5.loadFeatureIntervalTree(refName);
+
+                case 3:
+                  intervalTree = _context8.sent;
+                  intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) {
+                    return observer.next(f);
+                  });
+                  observer.complete();
+
+                case 6:
+                case "end":
+                  return _context8.stop();
+              }
+            }
+          }, _callee8);
+        }));
+
+        return function (_x3) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "freeResources",
+    value: function freeResources() {}
+  }]);
+  return BedAdapter;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports.default = BedAdapter;
+(0, _defineProperty2.default)(BedAdapter, "capabilities", ['getFeatures', 'getRefNames']);