@gmod/bbi 1.0.27 → 1.0.31

package/dist/bigwig.d.ts

@@ -1,5 +1,5 @@
 import { BlockView } from './blockView';
-import { BBI } from './bbi';
+import { BBI, RequestOptions } from './bbi';
 export declare class BigWig extends BBI {
     /**
      * Retrieves a BlockView of a specific zoomLevel
@@ -9,5 +9,5 @@ export declare class BigWig extends BBI {
      * @param end - The end of a region
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
-    protected getView(scale: number, abortSignal?: AbortSignal): Promise<BlockView>;
+    protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
 }

package/dist/bigwig.js

@@ -1,43 +1,64 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
+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 };
+    }
+};
+Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigWig = 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 _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _blockView = require("./blockView");
-
-var _bbi = require("./bbi");
-
-var BigWig =
-/*#__PURE__*/
-function (_BBI) {
-  (0, _inherits2.default)(BigWig, _BBI);
-
-  function BigWig() {
-    (0, _classCallCheck2.default)(this, BigWig);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BigWig).apply(this, arguments));
-  }
-
-  (0, _createClass2.default)(BigWig, [{
-    key: "getView",
-
+var blockView_1 = require("./blockView");
+var bbi_1 = require("./bbi");
+var BigWig = /** @class */ (function (_super) {
+    __extends(BigWig, _super);
+    function BigWig() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
     /**
      * Retrieves a BlockView of a specific zoomLevel
      *
@@ -46,77 +67,34 @@ function (_BBI) {
      * @param end - The end of a region
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
-    value: function () {
-      var _getView = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(scale, abortSignal) {
-        var _ref, zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize, basesPerPx, maxLevel, i, zh, indexLength;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.getHeader(abortSignal);
-
-              case 2:
-                _ref = _context.sent;
-                zoomLevels = _ref.zoomLevels;
-                refsByName = _ref.refsByName;
-                fileSize = _ref.fileSize;
-                isBigEndian = _ref.isBigEndian;
-                uncompressBufSize = _ref.uncompressBufSize;
-                basesPerPx = 1 / scale;
-                maxLevel = zoomLevels.length;
-
-                if (!fileSize) {
-                  // if we don't know the file size, we can't fetch the highest zoom level :-(
-                  maxLevel -= 1;
-                }
-
-                i = maxLevel;
-
-              case 12:
-                if (!(i >= 0)) {
-                  _context.next = 20;
-                  break;
+    BigWig.prototype.getView = function (scale, opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize, basesPerPx, maxLevel, i, zh, indexLength;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.getHeader(opts)];
+                    case 1:
+                        _a = _b.sent(), zoomLevels = _a.zoomLevels, refsByName = _a.refsByName, fileSize = _a.fileSize, isBigEndian = _a.isBigEndian, uncompressBufSize = _a.uncompressBufSize;
+                        basesPerPx = 1 / scale;
+                        maxLevel = zoomLevels.length;
+                        if (!fileSize) {
+                            // if we don't know the file size, we can't fetch the highest zoom level :-(
+                            maxLevel -= 1;
+                        }
+                        for (i = maxLevel; i >= 0; i -= 1) {
+                            zh = zoomLevels[i];
+                            if (zh && zh.reductionLevel <= 2 * basesPerPx) {
+                                indexLength = i < zoomLevels.length - 1
+                                    ? zoomLevels[i + 1].dataOffset - zh.indexOffset
+                                    : fileSize - 4 - zh.indexOffset;
+                                return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary')];
+                            }
+                        }
+                        return [2 /*return*/, this.getUnzoomedView(opts)];
                 }
-
-                zh = zoomLevels[i];
-
-                if (!(zh && zh.reductionLevel <= 2 * basesPerPx)) {
-                  _context.next = 17;
-                  break;
-                }
-
-                indexLength = i < zoomLevels.length - 1 ? zoomLevels[i + 1].dataOffset - zh.indexOffset : fileSize - 4 - zh.indexOffset;
-                return _context.abrupt("return", new _blockView.BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary'));
-
-              case 17:
-                i -= 1;
-                _context.next = 12;
-                break;
-
-              case 20:
-                return _context.abrupt("return", this.getUnzoomedView(abortSignal));
-
-              case 21:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getView(_x, _x2) {
-        return _getView.apply(this, arguments);
-      }
-
-      return getView;
-    }()
-  }]);
-  return BigWig;
-}(_bbi.BBI);
-
+            });
+        });
+    };
+    return BigWig;
+}(bbi_1.BBI));
 exports.BigWig = BigWig;
-//# sourceMappingURL=data:application/json;charset=utf-8;base64,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

package/dist/blockView.d.ts

@@ -1,4 +1,5 @@
 import { Observer } from 'rxjs';
+import { GenericFilehandle } from 'generic-filehandle';
 import { Feature } from './bbi';
 interface CoordRequest {
     chrId: number;
@@ -30,7 +31,7 @@ export declare class BlockView {
     private bigWigParser;
     private bigBedParser;
     private summaryParser;
-    constructor(bbi: any, refsByName: any, cirTreeOffset: number, cirTreeLength: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
+    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, cirTreeLength: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;