@gmod/bam 1.1.17 → 2.0.0

package/dist/bai.js

@@ -1,30 +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 __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) {
@@ -34,271 +8,204 @@ 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 virtualOffset_1 = require("./virtualOffset");
-var chunk_1 = __importDefault(require("./chunk"));
-var indexFile_1 = __importDefault(require("./indexFile"));
-var util_1 = require("./util");
-var BAI_MAGIC = 21578050; // BAI\1
+const virtualOffset_1 = require("./virtualOffset");
+const chunk_1 = __importDefault(require("./chunk"));
+const util_1 = require("./util");
+const indexFile_1 = __importDefault(require("./indexFile"));
+const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
 }
 function roundUp(n, multiple) {
     return n - (n % multiple) + multiple;
 }
-var BAI = /** @class */ (function (_super) {
-    __extends(BAI, _super);
-    function BAI() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    BAI.prototype.parsePseudoBin = function (bytes, offset) {
-        var lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 16, offset + 24), true));
-        return { lineCount: lineCount };
-    };
-    BAI.prototype.lineCount = function (refId, opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var prom, index, ret;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.parse(opts)];
-                    case 1:
-                        prom = _a.sent();
-                        index = prom.indices[refId];
-                        if (!index) {
-                            return [2 /*return*/, -1];
-                        }
-                        ret = index.stats || {};
-                        return [2 /*return*/, ret.lineCount === undefined ? -1 : ret.lineCount];
-                }
-            });
+function reg2bins(beg, end) {
+    end -= 1;
+    return [
+        [0, 0],
+        [1 + (beg >> 26), 1 + (end >> 26)],
+        [9 + (beg >> 23), 9 + (end >> 23)],
+        [73 + (beg >> 20), 73 + (end >> 20)],
+        [585 + (beg >> 17), 585 + (end >> 17)],
+        [4681 + (beg >> 14), 4681 + (end >> 14)],
+    ];
+}
+class BAI extends indexFile_1.default {
+    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;
         });
-    };
-    BAI.prototype.fetchBai = function (opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        if (!this.baiP) {
-            this.baiP = this.filehandle.readFile(opts).catch(function (e) {
-                _this.baiP = undefined;
-                throw e;
-            });
-        }
-        return this.baiP;
-    };
+    }
     // fetch and parse the index
-    BAI.prototype._parse = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, linearCount, linearIndex, k;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        data = { bai: true, maxBlockSize: 1 << 16 };
-                        return [4 /*yield*/, this.fetchBai()
-                            // check BAI magic numbers
-                        ];
-                    case 1:
-                        bytes = _a.sent();
-                        // check BAI magic numbers
-                        if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
-                            throw new Error('Not a BAI file');
-                        }
-                        data.refCount = bytes.readInt32LE(4);
-                        depth = 5;
-                        binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
-                        // read the indexes for each reference sequence
-                        data.indices = new Array(data.refCount);
-                        currOffset = 8;
-                        for (i = 0; i < data.refCount; i += 1) {
-                            binCount = bytes.readInt32LE(currOffset);
-                            stats = void 0;
-                            currOffset += 4;
-                            binIndex = {};
-                            for (j = 0; j < binCount; j += 1) {
-                                bin = bytes.readUInt32LE(currOffset);
-                                currOffset += 4;
-                                if (bin === binLimit + 1) {
-                                    currOffset += 4;
-                                    stats = this.parsePseudoBin(bytes, currOffset);
-                                    currOffset += 32;
-                                }
-                                else if (bin > binLimit + 1) {
-                                    throw new Error('bai index contains too many bins, please use CSI');
-                                }
-                                else {
-                                    chunkCount = bytes.readInt32LE(currOffset);
-                                    currOffset += 4;
-                                    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;
-                                }
-                            }
-                            linearCount = bytes.readInt32LE(currOffset);
-                            currOffset += 4;
-                            linearIndex = new Array(linearCount);
-                            for (k = 0; k < linearCount; k += 1) {
-                                linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                                currOffset += 8;
-                                this._findFirstData(data, linearIndex[k]);
-                            }
-                            data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
+    _parse(opts) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const bytes = (yield this.filehandle.readFile(opts));
+            // check BAI magic numbers
+            if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
+                throw new Error('Not a BAI file');
+            }
+            const refCount = bytes.readInt32LE(4);
+            const depth = 5;
+            const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
+            // read the indexes for each reference sequence
+            let curr = 8;
+            let firstDataLine;
+            const indices = new Array(refCount);
+            for (let i = 0; i < refCount; i++) {
+                // the binning index
+                const binCount = bytes.readInt32LE(curr);
+                let stats;
+                curr += 4;
+                const binIndex = {};
+                for (let j = 0; j < binCount; j += 1) {
+                    const bin = bytes.readUInt32LE(curr);
+                    curr += 4;
+                    if (bin === binLimit + 1) {
+                        curr += 4;
+                        stats = (0, util_1.parsePseudoBin)(bytes, curr + 16);
+                        curr += 32;
+                    }
+                    else if (bin > binLimit + 1) {
+                        throw new Error('bai index contains too many bins, please use CSI');
+                    }
+                    else {
+                        const chunkCount = bytes.readInt32LE(curr);
+                        curr += 4;
+                        const chunks = new Array(chunkCount);
+                        for (let k = 0; k < chunkCount; k++) {
+                            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);
                         }
-                        return [2 /*return*/, data];
+                        binIndex[bin] = chunks;
+                    }
                 }
-            });
-        });
-    };
-    BAI.prototype.indexCov = function (seqId, start, end, opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var v, range, indexData, seqIdx, _a, linearIndex, stats, e, s, depths, totalSize, currentPos, i, j;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        v = 16384;
-                        range = start !== undefined;
-                        return [4 /*yield*/, this.parse(opts)];
-                    case 1:
-                        indexData = _b.sent();
-                        seqIdx = indexData.indices[seqId];
-                        if (!seqIdx) {
-                            return [2 /*return*/, []];
-                        }
-                        _a = seqIdx.linearIndex, linearIndex = _a === void 0 ? [] : _a, stats = seqIdx.stats;
-                        if (!linearIndex.length) {
-                            return [2 /*return*/, []];
-                        }
-                        e = end !== undefined ? roundUp(end, v) : (linearIndex.length - 1) * v;
-                        s = start !== undefined ? roundDown(start, v) : 0;
-                        if (range) {
-                            depths = new Array((e - s) / v);
-                        }
-                        else {
-                            depths = new Array(linearIndex.length - 1);
-                        }
-                        totalSize = linearIndex[linearIndex.length - 1].blockPosition;
-                        if (e > (linearIndex.length - 1) * v) {
-                            throw new Error('query outside of range of linear index');
-                        }
-                        currentPos = linearIndex[s / v].blockPosition;
-                        for (i = s / v, j = 0; i < e / v; i++, j++) {
-                            depths[j] = {
-                                score: linearIndex[i + 1].blockPosition - currentPos,
-                                start: i * v,
-                                end: i * v + v,
-                            };
-                            currentPos = linearIndex[i + 1].blockPosition;
-                        }
-                        return [2 /*return*/, depths.map(function (d) {
-                                return __assign(__assign({}, d), { score: (d.score * stats.lineCount) / totalSize });
-                            })];
+                const linearCount = bytes.readInt32LE(curr);
+                curr += 4;
+                // as we're going through the linear index, figure out the smallest
+                // virtual offset in the indexes, which tells us where the BAM header
+                // ends
+                const linearIndex = new Array(linearCount);
+                for (let j = 0; j < linearCount; j++) {
+                    const offset = (0, virtualOffset_1.fromBytes)(bytes, curr);
+                    curr += 8;
+                    firstDataLine = (0, util_1.findFirstData)(firstDataLine, offset);
+                    linearIndex[j] = offset;
                 }
-            });
+                indices[i] = { binIndex, linearIndex, stats };
+            }
+            return {
+                bai: true,
+                firstDataLine,
+                maxBlockSize: 1 << 16,
+                indices,
+                refCount,
+            };
         });
-    };
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    BAI.prototype.reg2bins = function (beg, end) {
-        end -= 1;
-        return [
-            [0, 0],
-            [1 + (beg >> 26), 1 + (end >> 26)],
-            [9 + (beg >> 23), 9 + (end >> 23)],
-            [73 + (beg >> 20), 73 + (end >> 20)],
-            [585 + (beg >> 17), 585 + (end >> 17)],
-            [4681 + (beg >> 14), 4681 + (end >> 14)],
-        ];
-    };
-    BAI.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, nintv, lowest, minLin, maxLin, i, vp;
-            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();
-                        if (!indexData) {
-                            return [2 /*return*/, []];
-                        }
-                        ba = indexData.indices[refId];
-                        if (!ba) {
-                            return [2 /*return*/, []];
-                        }
-                        overlappingBins = this.reg2bins(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));
-                                    }
-                                }
-                            }
-                        }
-                        nintv = ba.linearIndex.length;
-                        lowest = null;
-                        minLin = Math.min(min >> 14, nintv - 1);
-                        maxLin = Math.min(max >> 14, nintv - 1);
-                        for (i = minLin; i <= maxLin; ++i) {
-                            vp = ba.linearIndex[i];
-                            if (vp) {
-                                if (!lowest || vp.compareTo(lowest) < 0) {
-                                    lowest = vp;
-                                }
-                            }
+    }
+    indexCov(seqId, start, end, opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const v = 16384;
+            const range = start !== undefined;
+            const indexData = yield this.parse(opts);
+            const seqIdx = indexData.indices[seqId];
+            if (!seqIdx) {
+                return [];
+            }
+            const { linearIndex = [], stats } = seqIdx;
+            if (linearIndex.length === 0) {
+                return [];
+            }
+            const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
+            const s = start === undefined ? 0 : roundDown(start, v);
+            const depths = range
+                ? new Array((e - s) / v)
+                : new Array(linearIndex.length - 1);
+            const totalSize = linearIndex[linearIndex.length - 1].blockPosition;
+            if (e > (linearIndex.length - 1) * v) {
+                throw new Error('query outside of range of linear index');
+            }
+            let currentPos = linearIndex[s / v].blockPosition;
+            for (let i = s / v, j = 0; i < e / v; i++, j++) {
+                depths[j] = {
+                    score: linearIndex[i + 1].blockPosition - currentPos,
+                    start: i * v,
+                    end: i * v + v,
+                };
+                currentPos = linearIndex[i + 1].blockPosition;
+            }
+            return depths.map(d => (Object.assign(Object.assign({}, d), { score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize })));
+        });
+    }
+    blocksForRange(refId, min, max, opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (min < 0) {
+                min = 0;
+            }
+            const indexData = yield this.parse(opts);
+            if (!indexData) {
+                return [];
+            }
+            const ba = indexData.indices[refId];
+            if (!ba) {
+                return [];
+            }
+            // List of bin #s that overlap min, max
+            const overlappingBins = reg2bins(min, max);
+            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 binChunk of binChunks) {
+                            chunks.push(binChunk);
                         }
-                        return [2 /*return*/, (0, util_1.optimizeChunks)(chunks, lowest)];
+                    }
                 }
-            });
+            }
+            // Use the linear index to find minimum file position of chunks that could
+            // contain alignments in the region
+            const nintv = ba.linearIndex.length;
+            let lowest;
+            const minLin = Math.min(min >> 14, nintv - 1);
+            const maxLin = Math.min(max >> 14, nintv - 1);
+            for (let i = minLin; i <= maxLin; ++i) {
+                const vp = ba.linearIndex[i];
+                if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                    lowest = vp;
+                }
+            }
+            return (0, util_1.optimizeChunks)(chunks, lowest);
+        });
+    }
+    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);
         });
-    };
-    return BAI;
-}(indexFile_1.default));
+    }
+}
 exports.default = BAI;
 //# sourceMappingURL=bai.js.map

package/dist/bai.js.map

@@ -1 +1 @@
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