@gmod/bam 1.1.17 → 2.0.0

package/dist/csi.js

@@ -1,19 +1,4 @@
 "use strict";
-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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -46,266 +31,165 @@ 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 };
-    }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var long_1 = __importDefault(require("long"));
-var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-var virtualOffset_1 = __importStar(require("./virtualOffset"));
-var chunk_1 = __importDefault(require("./chunk"));
-var util_1 = require("./util");
-var indexFile_1 = __importDefault(require("./indexFile"));
-var CSI1_MAGIC = 21582659; // CSI\1
-var CSI2_MAGIC = 38359875; // CSI\2
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const virtualOffset_1 = __importStar(require("./virtualOffset"));
+const chunk_1 = __importDefault(require("./chunk"));
+const util_1 = require("./util");
+const indexFile_1 = __importDefault(require("./indexFile"));
+const CSI1_MAGIC = 21582659; // CSI\1
+const CSI2_MAGIC = 38359875; // CSI\2
 function lshift(num, bits) {
     return num * Math.pow(2, bits);
 }
 function rshift(num, bits) {
     return Math.floor(num / Math.pow(2, bits));
 }
-var CSI = /** @class */ (function (_super) {
-    __extends(CSI, _super);
-    function CSI(args) {
-        var _this = _super.call(this, args) || this;
-        _this.maxBinNumber = 0;
-        _this.depth = 0;
-        _this.minShift = 0;
-        return _this;
+class CSI extends indexFile_1.default {
+    constructor() {
+        super(...arguments);
+        this.maxBinNumber = 0;
+        this.depth = 0;
+        this.minShift = 0;
     }
-    CSI.prototype.lineCount = function (refId) {
-        return __awaiter(this, void 0, void 0, function () {
-            var indexData, idx, stats;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.parse()];
-                    case 1:
-                        indexData = _a.sent();
-                        if (!indexData) {
-                            return [2 /*return*/, -1];
-                        }
-                        idx = indexData.indices[refId];
-                        if (!idx) {
-                            return [2 /*return*/, -1];
-                        }
-                        stats = indexData.indices[refId].stats;
-                        if (stats) {
-                            return [2 /*return*/, stats.lineCount];
-                        }
-                        return [2 /*return*/, -1];
-                }
-            });
+    lineCount(refId, opts) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            const indexData = yield this.parse(opts);
+            return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
         });
-    };
-    CSI.prototype.indexCov = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                return [2 /*return*/, []];
-            });
+    }
+    indexCov() {
+        return __awaiter(this, void 0, void 0, function* () {
+            return [];
         });
-    };
-    CSI.prototype.parseAuxData = function (bytes, offset, auxLength) {
-        if (auxLength < 30) {
-            return {};
-        }
-        var data = {};
-        data.formatFlags = bytes.readInt32LE(offset);
-        data.coordinateType =
-            data.formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
-        data.format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[data.formatFlags & 0xf];
-        if (!data.format) {
-            throw new Error("invalid Tabix preset format flags ".concat(data.formatFlags));
+    }
+    parseAuxData(bytes, offset) {
+        const formatFlags = bytes.readInt32LE(offset);
+        const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
+        const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
+        if (!format) {
+            throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
         }
-        data.columnNumbers = {
+        const columnNumbers = {
             ref: bytes.readInt32LE(offset + 4),
             start: bytes.readInt32LE(offset + 8),
             end: bytes.readInt32LE(offset + 12),
         };
-        data.metaValue = bytes.readInt32LE(offset + 16);
-        data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
-        data.skipLines = bytes.readInt32LE(offset + 20);
-        var nameSectionLength = bytes.readInt32LE(offset + 24);
-        Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
-        return data;
-    };
-    CSI.prototype._parseNameBytes = function (namesBytes) {
-        var currRefId = 0;
-        var currNameStart = 0;
-        var refIdToName = [];
-        var refNameToId = {};
-        for (var i = 0; i < namesBytes.length; i += 1) {
-            if (!namesBytes[i]) {
-                if (currNameStart < i) {
-                    var refName = namesBytes.toString('utf8', currNameStart, i);
-                    refName = this.renameRefSeq(refName);
-                    refIdToName[currRefId] = refName;
-                    refNameToId[refName] = currRefId;
-                }
-                currNameStart = i + 1;
-                currRefId += 1;
-            }
-        }
-        return { refNameToId: refNameToId, refIdToName: refIdToName };
-    };
+        const metaValue = bytes.readInt32LE(offset + 16);
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
+        const skipLines = bytes.readInt32LE(offset + 20);
+        const nameSectionLength = bytes.readInt32LE(offset + 24);
+        return Object.assign({ columnNumbers,
+            coordinateType,
+            metaValue,
+            metaChar,
+            skipLines,
+            format,
+            formatFlags }, (0, util_1.parseNameBytes)(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq));
+    }
     // fetch and parse the index
-    CSI.prototype._parse = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var data, buffer, bytes, auxLength, currOffset, i, binCount, binIndex, stats // < provided by parsing a pseudo-bin, if present
-            , j, bin, loffset, chunkCount, chunks, k, u, v;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        data = { csi: true, maxBlockSize: 1 << 16 };
-                        return [4 /*yield*/, this.filehandle.readFile(opts)];
-                    case 1:
-                        buffer = (_a.sent());
-                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)
-                            // check TBI magic numbers
-                        ];
-                    case 2:
-                        bytes = _a.sent();
-                        // check TBI magic numbers
-                        if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
-                            data.csiVersion = 1;
-                        }
-                        else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
-                            data.csiVersion = 2;
-                        }
-                        else {
-                            throw new Error('Not a CSI file');
-                            // TODO: do we need to support big-endian CSI files?
-                        }
-                        this.minShift = bytes.readInt32LE(4);
-                        this.depth = bytes.readInt32LE(8);
-                        this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
-                        auxLength = bytes.readInt32LE(12);
-                        if (auxLength) {
-                            Object.assign(data, this.parseAuxData(bytes, 16, auxLength));
-                        }
-                        data.refCount = bytes.readInt32LE(16 + auxLength);
-                        // read the indexes for each reference sequence
-                        data.indices = new Array(data.refCount);
-                        currOffset = 16 + auxLength + 4;
-                        i = 0;
-                        _a.label = 3;
-                    case 3:
-                        if (!(i < data.refCount)) return [3 /*break*/, 6];
-                        return [4 /*yield*/, (0, util_1.abortBreakPoint)(opts.signal)
-                            // the binning index
-                        ];
-                    case 4:
-                        _a.sent();
-                        binCount = bytes.readInt32LE(currOffset);
-                        currOffset += 4;
-                        binIndex = {};
-                        stats = void 0;
-                        for (j = 0; j < binCount; j += 1) {
-                            bin = bytes.readUInt32LE(currOffset);
-                            if (bin > this.maxBinNumber) {
-                                // this is a fake bin that actually has stats information
-                                // about the reference sequence in it
-                                stats = this.parsePseudoBin(bytes, currOffset + 4);
-                                currOffset += 4 + 8 + 4 + 16 + 16;
-                            }
-                            else {
-                                loffset = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 4);
-                                this._findFirstData(data, loffset);
-                                chunkCount = bytes.readInt32LE(currOffset + 12);
-                                currOffset += 16;
-                                chunks = new Array(chunkCount);
-                                for (k = 0; k < chunkCount; k += 1) {
-                                    u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                                    v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
-                                    currOffset += 16;
-                                    // this._findFirstData(data, u)
-                                    chunks[k] = new chunk_1.default(u, v, bin);
-                                }
-                                binIndex[bin] = chunks;
-                            }
+    _parse(opts) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const buffer = yield this.filehandle.readFile(opts);
+            const bytes = yield (0, bgzf_filehandle_1.unzip)(buffer);
+            let csiVersion;
+            // check TBI magic numbers
+            if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+                csiVersion = 1;
+            }
+            else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+                csiVersion = 2;
+            }
+            else {
+                throw new Error('Not a CSI file');
+                // TODO: do we need to support big-endian CSI files?
+            }
+            this.minShift = bytes.readInt32LE(4);
+            this.depth = bytes.readInt32LE(8);
+            this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+            const auxLength = bytes.readInt32LE(12);
+            const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
+            const refCount = bytes.readInt32LE(16 + auxLength);
+            // read the indexes for each reference sequence
+            let curr = 16 + auxLength + 4;
+            let firstDataLine;
+            const indices = new Array(refCount);
+            for (let i = 0; i < refCount; i++) {
+                // the binning index
+                const binCount = bytes.readInt32LE(curr);
+                curr += 4;
+                const binIndex = {};
+                let stats; // < provided by parsing a pseudo-bin, if present
+                for (let j = 0; j < binCount; j++) {
+                    const bin = bytes.readUInt32LE(curr);
+                    curr += 4;
+                    if (bin > this.maxBinNumber) {
+                        stats = (0, util_1.parsePseudoBin)(bytes, curr + 28);
+                        curr += 28 + 16;
+                    }
+                    else {
+                        firstDataLine = (0, util_1.findFirstData)(firstDataLine, (0, virtualOffset_1.fromBytes)(bytes, curr));
+                        curr += 8;
+                        const chunkCount = bytes.readInt32LE(curr);
+                        curr += 4;
+                        const chunks = new Array(chunkCount);
+                        for (let k = 0; k < chunkCount; k += 1) {
+                            const u = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            const v = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                            curr += 8;
+                            firstDataLine = (0, util_1.findFirstData)(firstDataLine, u);
+                            chunks[k] = new chunk_1.default(u, v, bin);
                         }
-                        data.indices[i] = { binIndex: binIndex, stats: stats };
-                        _a.label = 5;
-                    case 5:
-                        i += 1;
-                        return [3 /*break*/, 3];
-                    case 6: return [2 /*return*/, data];
+                        binIndex[bin] = chunks;
+                    }
                 }
-            });
+                indices[i] = { binIndex, stats };
+            }
+            return Object.assign({ csiVersion,
+                firstDataLine,
+                indices,
+                refCount, csi: true, maxBlockSize: 1 << 16 }, aux);
         });
-    };
-    CSI.prototype.parsePseudoBin = function (bytes, offset) {
-        var lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
-        return { lineCount: lineCount };
-    };
-    CSI.prototype.blocksForRange = function (refId, min, max, opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var indexData, ba, overlappingBins, chunks, _i, overlappingBins_1, _a, start, end, bin, binChunks, c;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        if (min < 0) {
-                            min = 0;
-                        }
-                        return [4 /*yield*/, this.parse(opts)];
-                    case 1:
-                        indexData = _b.sent();
-                        ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
-                        if (!ba) {
-                            return [2 /*return*/, []];
-                        }
-                        overlappingBins = this.reg2bins(min, max) // List of bin #s that overlap min, max
-                        ;
-                        chunks = [];
-                        // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
-                        for (_i = 0, overlappingBins_1 = overlappingBins; _i < overlappingBins_1.length; _i++) {
-                            _a = overlappingBins_1[_i], start = _a[0], end = _a[1];
-                            for (bin = start; bin <= end; bin++) {
-                                if (ba.binIndex[bin]) {
-                                    binChunks = ba.binIndex[bin];
-                                    for (c = 0; c < binChunks.length; ++c) {
-                                        chunks.push(new chunk_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
-                                    }
-                                }
-                            }
+    }
+    blocksForRange(refId, min, max, opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (min < 0) {
+                min = 0;
+            }
+            const indexData = yield this.parse(opts);
+            const ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
+            if (!ba) {
+                return [];
+            }
+            const overlappingBins = this.reg2bins(min, max);
+            if (overlappingBins.length === 0) {
+                return [];
+            }
+            const chunks = [];
+            // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+            for (const [start, end] of overlappingBins) {
+                for (let bin = start; bin <= end; bin++) {
+                    if (ba.binIndex[bin]) {
+                        const binChunks = ba.binIndex[bin];
+                        for (const c of binChunks) {
+                            chunks.push(c);
                         }
-                        return [2 /*return*/, (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0))];
+                    }
                 }
-            });
+            }
+            return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
         });
-    };
+    }
     /**
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open)
      */
-    CSI.prototype.reg2bins = function (beg, end) {
+    reg2bins(beg, end) {
         beg -= 1; // < convert to 1-based closed
         if (beg < 1) {
             beg = 1;
@@ -314,21 +198,38 @@ var CSI = /** @class */ (function (_super) {
             end = Math.pow(2, 34);
         } // 17 GiB ought to be enough for anybody
         end -= 1;
-        var l = 0;
-        var t = 0;
-        var s = this.minShift + this.depth * 3;
-        var bins = [];
+        let l = 0;
+        let t = 0;
+        let s = this.minShift + this.depth * 3;
+        const bins = [];
         for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
-            var b = t + rshift(beg, s);
-            var e = t + rshift(end, s);
+            const b = t + rshift(beg, s);
+            const e = t + rshift(end, s);
             if (e - b + bins.length > this.maxBinNumber) {
-                throw new Error("query ".concat(beg, "-").concat(end, " is too large for current binning scheme (shift ").concat(this.minShift, ", depth ").concat(this.depth, "), try a smaller query or a coarser index binning scheme"));
+                throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
             }
             bins.push([b, e]);
         }
         return bins;
-    };
-    return CSI;
-}(indexFile_1.default));
+    }
+    parse(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!this.setupP) {
+                this.setupP = this._parse(opts).catch(e => {
+                    this.setupP = undefined;
+                    throw e;
+                });
+            }
+            return this.setupP;
+        });
+    }
+    hasRefSeq(seqId, opts = {}) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            const header = yield this.parse(opts);
+            return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+        });
+    }
+}
 exports.default = CSI;
 //# sourceMappingURL=csi.js.map

package/dist/csi.js.map

@@ -1 +1 @@
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package/dist/errors.js

@@ -1,78 +1,33 @@
 "use strict";
-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 __());
-    };
-})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BamArgumentError = exports.BamSizeLimitError = exports.BamBufferOverrunError = exports.BamMalformedError = exports.BamUnimplementedError = exports.BamError = void 0;
-var BamError = /** @class */ (function (_super) {
-    __extends(BamError, _super);
-    function BamError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamError;
-}(Error));
+class BamError extends Error {
+}
 exports.BamError = BamError;
 /** Error caused by encountering a part of the BAM spec that has not yet been implemented */
-var BamUnimplementedError = /** @class */ (function (_super) {
-    __extends(BamUnimplementedError, _super);
-    function BamUnimplementedError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamUnimplementedError;
-}(Error));
+class BamUnimplementedError extends Error {
+}
 exports.BamUnimplementedError = BamUnimplementedError;
 /** An error caused by malformed data.  */
-var BamMalformedError = /** @class */ (function (_super) {
-    __extends(BamMalformedError, _super);
-    function BamMalformedError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamMalformedError;
-}(BamError));
+class BamMalformedError extends BamError {
+}
 exports.BamMalformedError = BamMalformedError;
 /**
  * An error caused by attempting to read beyond the end of the defined data.
  */
-var BamBufferOverrunError = /** @class */ (function (_super) {
-    __extends(BamBufferOverrunError, _super);
-    function BamBufferOverrunError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamBufferOverrunError;
-}(BamMalformedError));
+class BamBufferOverrunError extends BamMalformedError {
+}
 exports.BamBufferOverrunError = BamBufferOverrunError;
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-var BamSizeLimitError = /** @class */ (function (_super) {
-    __extends(BamSizeLimitError, _super);
-    function BamSizeLimitError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamSizeLimitError;
-}(BamError));
+class BamSizeLimitError extends BamError {
+}
 exports.BamSizeLimitError = BamSizeLimitError;
 /**
  * An invalid argument was supplied to a bam-js method or object.
  */
-var BamArgumentError = /** @class */ (function (_super) {
-    __extends(BamArgumentError, _super);
-    function BamArgumentError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return BamArgumentError;
-}(BamError));
+class BamArgumentError extends BamError {
+}
 exports.BamArgumentError = BamArgumentError;
 //# sourceMappingURL=errors.js.map

package/dist/errors.js.map

@@ -1 +1 @@
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