@gmod/bbi 2.0.4 → 3.0.0

package/dist/bbi.js

@@ -1,15 +1,4 @@
 "use strict";
-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) {
@@ -19,42 +8,15 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         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.BBI = void 0;
-var binary_parser_1 = require("binary-parser");
-var generic_filehandle_1 = require("generic-filehandle");
-var rxjs_1 = require("rxjs");
-var operators_1 = require("rxjs/operators");
-var blockView_1 = require("./blockView");
-var BIG_WIG_MAGIC = -2003829722;
-var BIG_BED_MAGIC = -2021002517;
+const binary_parser_1 = require("binary-parser");
+const generic_filehandle_1 = require("generic-filehandle");
+const rxjs_1 = require("rxjs");
+const operators_1 = require("rxjs/operators");
+const blockView_1 = require("./blockView");
+const BIG_WIG_MAGIC = -2003829722;
+const BIG_BED_MAGIC = -2021002517;
 function toString(arr) {
     return new TextDecoder().decode(arr);
 }
@@ -64,8 +26,8 @@ function toString(arr) {
  * @return an object with compiled parsers
  */
 function getParsers(isBE) {
-    var le = isBE ? 'big' : 'little';
-    var headerParser = new binary_parser_1.Parser()
+    const le = isBE ? 'big' : 'little';
+    const headerParser = new binary_parser_1.Parser()
         .endianess(le)
         .int32('magic')
         .uint16('version')
@@ -88,43 +50,56 @@ function getParsers(isBE) {
             .uint64('dataOffset')
             .uint64('indexOffset'),
     });
-    var totalSummaryParser = new binary_parser_1.Parser()
+    const totalSummaryParser = new binary_parser_1.Parser()
         .endianess(le)
         .uint64('basesCovered')
         .doublele('scoreMin')
         .doublele('scoreMax')
         .doublele('scoreSum')
         .doublele('scoreSumSquares');
-    var chromTreeParser = new binary_parser_1.Parser()
+    const chromTreeParser = new binary_parser_1.Parser()
         .endianess(le)
         .uint32('magic')
         .uint32('blockSize')
         .uint32('keySize')
         .uint32('valSize')
         .uint64('itemCount');
-    var isLeafNode = new binary_parser_1.Parser()
+    const isLeafNode = new binary_parser_1.Parser()
         .endianess(le)
         .uint8('isLeafNode')
         .skip(1)
         .uint16('cnt')
         .saveOffset('offset');
     return {
-        chromTreeParser: chromTreeParser,
-        totalSummaryParser: totalSummaryParser,
-        headerParser: headerParser,
-        isLeafNode: isLeafNode,
+        chromTreeParser,
+        totalSummaryParser,
+        headerParser,
+        isLeafNode,
     };
 }
-var BBI = /** @class */ (function () {
+class BBI {
+    /* fetch and parse header information from a bigwig or bigbed file
+     * @param abortSignal - abort the operation, can be null
+     * @return a Header object
+     */
+    getHeader(opts = {}) {
+        const options = 'aborted' in opts ? { signal: opts } : opts;
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     /*
      * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
      * @param path - a Local file path as a string
      * @param url - a URL string
      * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
      */
-    function BBI(options) {
-        if (options === void 0) { options = {}; }
-        var filehandle = options.filehandle, _a = options.renameRefSeqs, renameRefSeqs = _a === void 0 ? function (s) { return s; } : _a, path = options.path, url = options.url;
+    constructor(options = {}) {
+        const { filehandle, renameRefSeqs = s => s, path, url } = options;
         this.renameRefSeqs = renameRefSeqs;
         if (filehandle) {
             this.bbi = filehandle;
@@ -139,74 +114,41 @@ var BBI = /** @class */ (function () {
             throw new Error('no file given');
         }
     }
-    /* fetch and parse header information from a bigwig or bigbed file
-     * @param abortSignal - abort the operation, can be null
-     * @return a Header object
-     */
-    BBI.prototype.getHeader = function (opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        var options = 'aborted' in opts ? { signal: opts } : opts;
-        if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(function (e) {
-                _this.headerP = undefined;
-                throw e;
-            });
-        }
-        return this.headerP;
-    };
-    BBI.prototype._getHeader = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var header, chroms;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this._getMainHeader(opts)];
-                    case 1:
-                        header = _a.sent();
-                        return [4 /*yield*/, this._readChromTree(header, opts)];
-                    case 2:
-                        chroms = _a.sent();
-                        return [2 /*return*/, __assign(__assign({}, header), chroms)];
-                }
-            });
+    _getHeader(opts) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const header = yield this._getMainHeader(opts);
+            const chroms = yield this._readChromTree(header, opts);
+            return Object.assign(Object.assign({}, header), chroms);
         });
-    };
-    BBI.prototype._getMainHeader = function (opts, requestSize) {
-        if (requestSize === void 0) { requestSize = 2000; }
-        return __awaiter(this, void 0, void 0, function () {
-            var buffer, isBigEndian, ret, header, magic, asOffset, totalSummaryOffset, off, tail, sum;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.bbi.read(Buffer.alloc(requestSize), 0, requestSize, 0, opts)];
-                    case 1:
-                        buffer = (_a.sent()).buffer;
-                        isBigEndian = this._isBigEndian(buffer);
-                        ret = getParsers(isBigEndian);
-                        header = ret.headerParser.parse(buffer);
-                        magic = header.magic, asOffset = header.asOffset, totalSummaryOffset = header.totalSummaryOffset;
-                        header.fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
-                        if (asOffset > requestSize || totalSummaryOffset > requestSize) {
-                            return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
-                        }
-                        if (asOffset) {
-                            off = Number(header.asOffset);
-                            header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
-                        }
-                        if (header.totalSummaryOffset > requestSize) {
-                            return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
-                        }
-                        if (header.totalSummaryOffset) {
-                            tail = buffer.subarray(Number(header.totalSummaryOffset));
-                            sum = ret.totalSummaryParser.parse(tail);
-                            header.totalSummary = __assign(__assign({}, sum), { basesCovered: Number(sum.basesCovered) });
-                        }
-                        return [2 /*return*/, __assign(__assign({}, header), { isBigEndian: isBigEndian })];
-                }
-            });
+    }
+    _getMainHeader(opts, requestSize = 2000) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const { buffer } = yield this.bbi.read(Buffer.alloc(requestSize), 0, requestSize, 0, opts);
+            const isBigEndian = this._isBigEndian(buffer);
+            const ret = getParsers(isBigEndian);
+            const header = ret.headerParser.parse(buffer);
+            const { magic, asOffset, totalSummaryOffset } = header;
+            header.fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
+            if (asOffset > requestSize || totalSummaryOffset > requestSize) {
+                return this._getMainHeader(opts, requestSize * 2);
+            }
+            if (asOffset) {
+                const off = Number(header.asOffset);
+                header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
+            }
+            if (header.totalSummaryOffset > requestSize) {
+                return this._getMainHeader(opts, requestSize * 2);
+            }
+            if (header.totalSummaryOffset) {
+                const tail = buffer.subarray(Number(header.totalSummaryOffset));
+                const sum = ret.totalSummaryParser.parse(tail);
+                header.totalSummary = Object.assign(Object.assign({}, sum), { basesCovered: Number(sum.basesCovered) });
+            }
+            return Object.assign(Object.assign({}, header), { isBigEndian });
         });
-    };
-    BBI.prototype._isBigEndian = function (buffer) {
-        var ret = buffer.readInt32LE(0);
+    }
+    _isBigEndian(buffer) {
+        let ret = buffer.readInt32LE(0);
         if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
             return false;
         }
@@ -215,108 +157,82 @@ var BBI = /** @class */ (function () {
             return true;
         }
         throw new Error('not a BigWig/BigBed file');
-    };
+    }
     // todo: add progress if long running
-    BBI.prototype._readChromTree = function (header, opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var isBE, le, refsByNumber, refsByName, unzoomedDataOffset, chromTreeOffset, off, buffer, p, keySize, leafNodeParser, nonleafNodeParser, rootNodeOffset, bptReadNode;
-            var _this = this;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        isBE = header.isBigEndian;
-                        le = isBE ? 'big' : 'little';
-                        refsByNumber = [];
-                        refsByName = {};
-                        unzoomedDataOffset = Number(header.unzoomedDataOffset);
-                        chromTreeOffset = Number(header.chromTreeOffset);
-                        while (unzoomedDataOffset % 4 !== 0) {
-                            unzoomedDataOffset += 1;
-                        }
-                        off = unzoomedDataOffset - chromTreeOffset;
-                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts)];
-                    case 1:
-                        buffer = (_a.sent()).buffer;
-                        p = getParsers(isBE);
-                        keySize = p.chromTreeParser.parse(buffer).keySize;
-                        leafNodeParser = new binary_parser_1.Parser()
-                            .endianess(le)
-                            .string('key', { stripNull: true, length: keySize })
-                            .uint32('refId')
-                            .uint32('refSize')
-                            .saveOffset('offset');
-                        nonleafNodeParser = new binary_parser_1.Parser()
-                            .endianess(le)
-                            .skip(keySize)
-                            .uint64('childOffset')
-                            .saveOffset('offset');
-                        rootNodeOffset = 32;
-                        bptReadNode = function (currentOffset) { return __awaiter(_this, void 0, void 0, function () {
-                            var offset, ret, isLeafNode, cnt, n, leafRet, key, refId, refSize, refRec, nextNodes, n, nonleafRet, childOffset;
-                            return __generator(this, function (_a) {
-                                switch (_a.label) {
-                                    case 0:
-                                        offset = currentOffset;
-                                        if (offset >= buffer.length) {
-                                            throw new Error('reading beyond end of buffer');
-                                        }
-                                        ret = p.isLeafNode.parse(buffer.subarray(offset));
-                                        isLeafNode = ret.isLeafNode, cnt = ret.cnt;
-                                        offset += ret.offset;
-                                        if (!isLeafNode) return [3 /*break*/, 1];
-                                        for (n = 0; n < cnt; n += 1) {
-                                            leafRet = leafNodeParser.parse(buffer.subarray(offset));
-                                            offset += leafRet.offset;
-                                            key = leafRet.key, refId = leafRet.refId, refSize = leafRet.refSize;
-                                            refRec = { name: key, id: refId, length: refSize };
-                                            refsByName[this.renameRefSeqs(key)] = refId;
-                                            refsByNumber[refId] = refRec;
-                                        }
-                                        return [3 /*break*/, 3];
-                                    case 1:
-                                        nextNodes = [];
-                                        for (n = 0; n < cnt; n += 1) {
-                                            nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset));
-                                            childOffset = nonleafRet.childOffset;
-                                            offset += nonleafRet.offset;
-                                            nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
-                                        }
-                                        return [4 /*yield*/, Promise.all(nextNodes)];
-                                    case 2:
-                                        _a.sent();
-                                        _a.label = 3;
-                                    case 3: return [2 /*return*/];
-                                }
-                            });
-                        }); };
-                        return [4 /*yield*/, bptReadNode(rootNodeOffset)];
-                    case 2:
-                        _a.sent();
-                        return [2 /*return*/, {
-                                refsByName: refsByName,
-                                refsByNumber: refsByNumber,
-                            }];
+    _readChromTree(header, opts) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const isBE = header.isBigEndian;
+            const le = isBE ? 'big' : 'little';
+            const refsByNumber = [];
+            const refsByName = {};
+            let unzoomedDataOffset = Number(header.unzoomedDataOffset);
+            const chromTreeOffset = Number(header.chromTreeOffset);
+            while (unzoomedDataOffset % 4 !== 0) {
+                unzoomedDataOffset += 1;
+            }
+            const off = unzoomedDataOffset - chromTreeOffset;
+            const { buffer } = yield this.bbi.read(Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
+            const p = getParsers(isBE);
+            const { keySize } = p.chromTreeParser.parse(buffer);
+            const leafNodeParser = new binary_parser_1.Parser()
+                .endianess(le)
+                .string('key', { stripNull: true, length: keySize })
+                .uint32('refId')
+                .uint32('refSize')
+                .saveOffset('offset');
+            const nonleafNodeParser = new binary_parser_1.Parser()
+                .endianess(le)
+                .skip(keySize)
+                .uint64('childOffset')
+                .saveOffset('offset');
+            const rootNodeOffset = 32;
+            const bptReadNode = (currentOffset) => __awaiter(this, void 0, void 0, function* () {
+                let offset = currentOffset;
+                if (offset >= buffer.length) {
+                    throw new Error('reading beyond end of buffer');
+                }
+                const ret = p.isLeafNode.parse(buffer.subarray(offset));
+                const { isLeafNode, cnt } = ret;
+                offset += ret.offset;
+                if (isLeafNode) {
+                    for (let n = 0; n < cnt; n += 1) {
+                        const leafRet = leafNodeParser.parse(buffer.subarray(offset));
+                        offset += leafRet.offset;
+                        const { key, refId, refSize } = leafRet;
+                        const refRec = { name: key, id: refId, length: refSize };
+                        refsByName[this.renameRefSeqs(key)] = refId;
+                        refsByNumber[refId] = refRec;
+                    }
+                }
+                else {
+                    // parse index node
+                    const nextNodes = [];
+                    for (let n = 0; n < cnt; n += 1) {
+                        const nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset));
+                        const { childOffset } = nonleafRet;
+                        offset += nonleafRet.offset;
+                        nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
+                    }
+                    yield Promise.all(nextNodes);
                 }
             });
+            yield bptReadNode(rootNodeOffset);
+            return {
+                refsByName,
+                refsByNumber,
+            };
         });
-    };
+    }
     /*
      * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
      * @param abortSignal - a signal to optionally abort this operation
      */
-    BBI.prototype.getUnzoomedView = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.getHeader(opts)];
-                    case 1:
-                        _a = _b.sent(), unzoomedIndexOffset = _a.unzoomedIndexOffset, refsByName = _a.refsByName, uncompressBufSize = _a.uncompressBufSize, isBigEndian = _a.isBigEndian, fileType = _a.fileType;
-                        return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType)];
-                }
-            });
+    getUnzoomedView(opts) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = yield this.getHeader(opts);
+            return new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
         });
-    };
+    }
     /**
      * Gets features from a BigWig file
      *
@@ -325,66 +241,39 @@ var BBI = /** @class */ (function () {
      * @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
      */
-    BBI.prototype.getFeatureStream = function (refName, start, end, opts) {
-        if (opts === void 0) { opts = {
-            scale: 1,
-        }; }
-        return __awaiter(this, void 0, void 0, function () {
-            var chrName, view;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getHeader(opts)];
-                    case 1:
-                        _a.sent();
-                        chrName = this.renameRefSeqs(refName);
-                        if (!opts.basesPerSpan) return [3 /*break*/, 3];
-                        return [4 /*yield*/, this.getView(1 / opts.basesPerSpan, opts)];
-                    case 2:
-                        view = _a.sent();
-                        return [3 /*break*/, 7];
-                    case 3:
-                        if (!opts.scale) return [3 /*break*/, 5];
-                        return [4 /*yield*/, this.getView(opts.scale, opts)];
-                    case 4:
-                        view = _a.sent();
-                        return [3 /*break*/, 7];
-                    case 5: return [4 /*yield*/, this.getView(1, opts)];
-                    case 6:
-                        view = _a.sent();
-                        _a.label = 7;
-                    case 7:
-                        if (!view) {
-                            throw new Error('unable to get block view for data');
-                        }
-                        return [2 /*return*/, new rxjs_1.Observable(function (observer) {
-                                view.readWigData(chrName, start, end, observer, opts);
-                            })];
-                }
+    getFeatureStream(refName, start, end, opts = {
+        scale: 1,
+    }) {
+        return __awaiter(this, void 0, void 0, function* () {
+            yield this.getHeader(opts);
+            const chrName = this.renameRefSeqs(refName);
+            let view;
+            if (opts.basesPerSpan) {
+                view = yield this.getView(1 / opts.basesPerSpan, opts);
+            }
+            else if (opts.scale) {
+                view = yield this.getView(opts.scale, opts);
+            }
+            else {
+                view = yield this.getView(1, opts);
+            }
+            if (!view) {
+                throw new Error('unable to get block view for data');
+            }
+            return new rxjs_1.Observable((observer) => {
+                view.readWigData(chrName, start, end, observer, opts);
             });
         });
-    };
-    BBI.prototype.getFeatures = function (refName, start, end, opts) {
-        if (opts === void 0) { opts = {
-            scale: 1,
-        }; }
-        return __awaiter(this, void 0, void 0, function () {
-            var ob, ret;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getFeatureStream(refName, start, end, opts)];
-                    case 1:
-                        ob = _a.sent();
-                        return [4 /*yield*/, ob
-                                .pipe((0, operators_1.reduce)(function (acc, curr) { return acc.concat(curr); }))
-                                .toPromise()];
-                    case 2:
-                        ret = _a.sent();
-                        return [2 /*return*/, ret || []];
-                }
-            });
+    }
+    getFeatures(refName, start, end, opts = {
+        scale: 1,
+    }) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const ob = yield this.getFeatureStream(refName, start, end, opts);
+            const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
+            return ret.flat();
         });
-    };
-    return BBI;
-}());
+    }
+}
 exports.BBI = BBI;
 //# sourceMappingURL=bbi.js.map

package/dist/bbi.js.map

@@ -1 +1 @@
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