@jbrowse/plugin-alignments 2.1.0 → 2.1.2

package/dist/BamAdapter/BamAdapter.js

@@ -1,358 +1,179 @@
 "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 __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 };
-    }
-};
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var bam_1 = require("@gmod/bam");
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var util_1 = require("@jbrowse/core/util");
-var io_1 = require("@jbrowse/core/util/io");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var operators_1 = require("rxjs/operators");
-var configuration_1 = require("@jbrowse/core/configuration");
-var BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
-var BamAdapter = /** @class */ (function (_super) {
-    __extends(BamAdapter, _super);
-    function BamAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
+const bam_1 = require("@gmod/bam");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const operators_1 = require("rxjs/operators");
+const configuration_1 = require("@jbrowse/core/configuration");
+const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
+class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
-    BamAdapter.prototype.configure = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var bamLocation, location_1, indexType, bam_2, adapterConfig;
-            return __generator(this, function (_a) {
-                if (!this.configured) {
-                    bamLocation = (0, configuration_1.readConfObject)(this.config, 'bamLocation');
-                    location_1 = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
-                    indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
-                    bam_2 = new bam_1.BamFile({
-                        bamFilehandle: (0, io_1.openLocation)(bamLocation, this.pluginManager),
-                        csiFilehandle: indexType === 'CSI'
-                            ? (0, io_1.openLocation)(location_1, this.pluginManager)
-                            : undefined,
-                        baiFilehandle: indexType !== 'CSI'
-                            ? (0, io_1.openLocation)(location_1, this.pluginManager)
-                            : undefined,
-                        // chunkSizeLimit and fetchSizeLimit are more troublesome than
-                        // helpful, and have given overly large values on the ultra long
-                        // nanopore reads even with 500MB limits, so disabled with infinity
-                        chunkSizeLimit: Infinity,
-                        fetchSizeLimit: Infinity,
-                        yieldThreadTime: Infinity,
-                    });
-                    adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-                    if (adapterConfig && this.getSubAdapter) {
-                        this.configured = this.getSubAdapter(adapterConfig).then(function (_a) {
-                            var dataAdapter = _a.dataAdapter;
-                            return ({
-                                bam: bam_2,
-                                sequenceAdapter: dataAdapter,
-                            });
-                        });
-                    }
-                    else {
-                        this.configured = Promise.resolve({ bam: bam_2 });
-                    }
-                }
-                return [2 /*return*/, this.configured];
+    async configure() {
+        if (!this.configured) {
+            const bamLocation = (0, configuration_1.readConfObject)(this.config, 'bamLocation');
+            const location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
+            const indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
+            const bam = new bam_1.BamFile({
+                bamFilehandle: (0, io_1.openLocation)(bamLocation, this.pluginManager),
+                csiFilehandle: indexType === 'CSI'
+                    ? (0, io_1.openLocation)(location, this.pluginManager)
+                    : undefined,
+                baiFilehandle: indexType !== 'CSI'
+                    ? (0, io_1.openLocation)(location, this.pluginManager)
+                    : undefined,
+                // chunkSizeLimit and fetchSizeLimit are more troublesome than
+                // helpful, and have given overly large values on the ultra long
+                // nanopore reads even with 500MB limits, so disabled with infinity
+                chunkSizeLimit: Infinity,
+                fetchSizeLimit: Infinity,
+                yieldThreadTime: Infinity,
             });
-        });
-    };
-    BamAdapter.prototype.getHeader = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var bam;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        bam = (_a.sent()).bam;
-                        return [2 /*return*/, bam.getHeaderText(opts)];
-                }
+            const adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
+            if (adapterConfig && this.getSubAdapter) {
+                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => ({
+                    bam,
+                    sequenceAdapter: dataAdapter,
+                }));
+            }
+            else {
+                this.configured = Promise.resolve({ bam });
+            }
+        }
+        return this.configured;
+    }
+    async getHeader(opts) {
+        const { bam } = await this.configure();
+        return bam.getHeaderText(opts);
+    }
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const { bam } = await this.configure();
+        this.samHeader = await (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
+            const samHeader = await bam.getHeader(opts);
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ref ID numbers and names
+            const idToName = [];
+            const nameToId = {};
+            samHeader
+                .filter(l => l.tag === 'SQ')
+                .forEach((sqLine, refId) => {
+                sqLine.data.forEach(item => {
+                    if (item.tag === 'SN') {
+                        // this is the ref name
+                        const refName = item.value;
+                        nameToId[refName] = refId;
+                        idToName[refId] = refName;
+                    }
+                });
             });
+            return { idToName, nameToId };
         });
-    };
-    BamAdapter.prototype.setupPre = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, statusCallback, bam, _b;
-            var _this = this;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        _a = (opts || {}).statusCallback, statusCallback = _a === void 0 ? function () { } : _a;
-                        return [4 /*yield*/, this.configure()];
-                    case 1:
-                        bam = (_c.sent()).bam;
-                        _b = this;
-                        return [4 /*yield*/, (0, util_1.updateStatus)('Downloading index', statusCallback, function () { return __awaiter(_this, void 0, void 0, function () {
-                                var samHeader, idToName, nameToId;
-                                return __generator(this, function (_a) {
-                                    switch (_a.label) {
-                                        case 0: return [4 /*yield*/, bam.getHeader(opts)
-                                            // use the @SQ lines in the header to figure out the
-                                            // mapping between ref ref ID numbers and names
-                                        ];
-                                        case 1:
-                                            samHeader = _a.sent();
-                                            idToName = [];
-                                            nameToId = {};
-                                            samHeader
-                                                .filter(function (l) { return l.tag === 'SQ'; })
-                                                .forEach(function (sqLine, refId) {
-                                                sqLine.data.forEach(function (item) {
-                                                    if (item.tag === 'SN') {
-                                                        // this is the ref name
-                                                        var refName = item.value;
-                                                        nameToId[refName] = refId;
-                                                        idToName[refId] = refName;
-                                                    }
-                                                });
-                                            });
-                                            return [2 /*return*/, { idToName: idToName, nameToId: nameToId }];
-                                    }
-                                });
-                            }); })];
-                    case 2:
-                        _b.samHeader = _c.sent();
-                        return [2 /*return*/, this.samHeader];
-                }
+        return this.samHeader;
+    }
+    async setup(opts) {
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
             });
+        }
+        return this.setupP;
+    }
+    async getRefNames(opts) {
+        const { idToName } = await this.setup(opts);
+        return idToName;
+    }
+    async seqFetch(refName, start, end) {
+        const { sequenceAdapter } = await this.configure();
+        const refSeqStore = sequenceAdapter;
+        if (!refSeqStore) {
+            return undefined;
+        }
+        if (!refName) {
+            return undefined;
+        }
+        const features = refSeqStore.getFeatures({
+            refName,
+            start,
+            end,
+            assemblyName: '',
         });
-    };
-    BamAdapter.prototype.setup = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.setupP) {
-                    this.setupP = this.setupPre(opts).catch(function (e) {
-                        _this.setupP = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.setupP];
-            });
+        const seqChunks = await features.pipe((0, operators_1.toArray)()).toPromise();
+        let sequence = '';
+        seqChunks
+            .sort((a, b) => a.get('start') - b.get('start'))
+            .forEach(chunk => {
+            const chunkStart = chunk.get('start');
+            const chunkEnd = chunk.get('end');
+            const trimStart = Math.max(start - chunkStart, 0);
+            const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
+            const trimLength = trimEnd - trimStart;
+            const chunkSeq = chunk.get('seq') || chunk.get('residues');
+            sequence += chunkSeq.substr(trimStart, trimLength);
         });
-    };
-    BamAdapter.prototype.getRefNames = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var idToName;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup(opts)];
-                    case 1:
-                        idToName = (_a.sent()).idToName;
-                        return [2 /*return*/, idToName];
+        if (sequence.length !== end - start) {
+            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
+        }
+        return sequence;
+    }
+    getFeatures(region, opts) {
+        const { refName, start, end, originalRefName } = region;
+        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { bam } = await this.configure();
+            await this.setup(opts);
+            statusCallback('Downloading alignments');
+            const records = await bam.getRecordsForRange(refName, start, end, opts);
+            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+            for (const record of records) {
+                let ref;
+                if (!record.get('MD')) {
+                    ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
                 }
-            });
-        });
-    };
-    BamAdapter.prototype.seqFetch = function (refName, start, end) {
-        return __awaiter(this, void 0, void 0, function () {
-            var sequenceAdapter, refSeqStore, features, seqChunks, sequence;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        sequenceAdapter = (_a.sent()).sequenceAdapter;
-                        refSeqStore = sequenceAdapter;
-                        if (!refSeqStore) {
-                            return [2 /*return*/, undefined];
-                        }
-                        if (!refName) {
-                            return [2 /*return*/, undefined];
-                        }
-                        features = refSeqStore.getFeatures({
-                            refName: refName,
-                            start: start,
-                            end: end,
-                            assemblyName: '',
-                        });
-                        return [4 /*yield*/, features.pipe((0, operators_1.toArray)()).toPromise()];
-                    case 2:
-                        seqChunks = _a.sent();
-                        sequence = '';
-                        seqChunks
-                            .sort(function (a, b) { return a.get('start') - b.get('start'); })
-                            .forEach(function (chunk) {
-                            var chunkStart = chunk.get('start');
-                            var chunkEnd = chunk.get('end');
-                            var trimStart = Math.max(start - chunkStart, 0);
-                            var trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
-                            var trimLength = trimEnd - trimStart;
-                            var chunkSeq = chunk.get('seq') || chunk.get('residues');
-                            sequence += chunkSeq.substr(trimStart, trimLength);
-                        });
-                        if (sequence.length !== end - start) {
-                            throw new Error("sequence fetch failed: fetching ".concat(refName, ":").concat((start - 1).toLocaleString(), "-").concat(end.toLocaleString(), " returned ").concat(sequence.length.toLocaleString(), " bases, but should have returned ").concat((end - start).toLocaleString()));
-                        }
-                        return [2 /*return*/, sequence];
+                const flags = record.flags;
+                if (!((flags & flagInclude) === flagInclude && !(flags & flagExclude))) {
+                    continue;
                 }
-            });
-        });
-    };
-    BamAdapter.prototype.getFeatures = function (region, opts) {
-        var _this = this;
-        var refName = region.refName, start = region.start, end = region.end, originalRefName = region.originalRefName;
-        var _a = opts || {}, signal = _a.signal, filterBy = _a.filterBy, _b = _a.statusCallback, statusCallback = _b === void 0 ? function () { } : _b;
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var bam, records, _a, _b, flagInclude, _c, flagExclude, tagFilter, readName, records_1, records_1_1, record, ref, flags, val, e_1_1;
-            var e_1, _d;
-            return __generator(this, function (_e) {
-                switch (_e.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        bam = (_e.sent()).bam;
-                        return [4 /*yield*/, this.setup(opts)];
-                    case 2:
-                        _e.sent();
-                        statusCallback('Downloading alignments');
-                        return [4 /*yield*/, bam.getRecordsForRange(refName, start, end, opts)];
-                    case 3:
-                        records = _e.sent();
-                        _a = filterBy || {}, _b = _a.flagInclude, flagInclude = _b === void 0 ? 0 : _b, _c = _a.flagExclude, flagExclude = _c === void 0 ? 0 : _c, tagFilter = _a.tagFilter, readName = _a.readName;
-                        _e.label = 4;
-                    case 4:
-                        _e.trys.push([4, 10, 11, 12]);
-                        records_1 = __values(records), records_1_1 = records_1.next();
-                        _e.label = 5;
-                    case 5:
-                        if (!!records_1_1.done) return [3 /*break*/, 9];
-                        record = records_1_1.value;
-                        ref = void 0;
-                        if (!!record.get('MD')) return [3 /*break*/, 7];
-                        return [4 /*yield*/, this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'))];
-                    case 6:
-                        ref = _e.sent();
-                        _e.label = 7;
-                    case 7:
-                        flags = record.flags;
-                        if (!((flags & flagInclude) === flagInclude && !(flags & flagExclude))) {
-                            return [3 /*break*/, 8];
-                        }
-                        if (tagFilter) {
-                            val = record.get(tagFilter.tag);
-                            if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
-                                return [3 /*break*/, 8];
-                            }
-                        }
-                        if (readName && record.get('name') !== readName) {
-                            return [3 /*break*/, 8];
-                        }
-                        observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
-                        _e.label = 8;
-                    case 8:
-                        records_1_1 = records_1.next();
-                        return [3 /*break*/, 5];
-                    case 9: return [3 /*break*/, 12];
-                    case 10:
-                        e_1_1 = _e.sent();
-                        e_1 = { error: e_1_1 };
-                        return [3 /*break*/, 12];
-                    case 11:
-                        try {
-                            if (records_1_1 && !records_1_1.done && (_d = records_1.return)) _d.call(records_1);
-                        }
-                        finally { if (e_1) throw e_1.error; }
-                        return [7 /*endfinally*/];
-                    case 12:
-                        statusCallback('');
-                        observer.complete();
-                        return [2 /*return*/];
+                if (tagFilter) {
+                    const val = record.get(tagFilter.tag);
+                    if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
+                        continue;
+                    }
                 }
-            });
-        }); }, signal);
-    };
-    BamAdapter.prototype.estimateRegionsStats = function (regions, opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var bam, bytes, fetchSizeLimit;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()
-                        // this is a method to avoid calling on htsget adapters
-                        // @ts-ignore
-                    ];
-                    case 1:
-                        bam = (_a.sent()).bam;
-                        if (!(bam.index.filehandle !== '?')) return [3 /*break*/, 3];
-                        return [4 /*yield*/, (0, util_1.bytesForRegions)(regions, bam)];
-                    case 2:
-                        bytes = _a.sent();
-                        fetchSizeLimit = (0, configuration_1.readConfObject)(this.config, 'fetchSizeLimit');
-                        return [2 /*return*/, { bytes: bytes, fetchSizeLimit: fetchSizeLimit }];
-                    case 3: return [2 /*return*/, _super.prototype.estimateRegionsStats.call(this, regions, opts)];
+                if (readName && record.get('name') !== readName) {
+                    continue;
                 }
-            });
-        });
-    };
-    BamAdapter.prototype.freeResources = function ( /* { region } */) { };
+                observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
+            }
+            statusCallback('');
+            observer.complete();
+        }, signal);
+    }
+    async estimateRegionsStats(regions, opts) {
+        const { bam } = await this.configure();
+        // this is a method to avoid calling on htsget adapters
+        // @ts-ignore
+        if (bam.index.filehandle !== '?') {
+            const bytes = await (0, util_1.bytesForRegions)(regions, bam);
+            const fetchSizeLimit = (0, configuration_1.readConfObject)(this.config, 'fetchSizeLimit');
+            return { bytes, fetchSizeLimit };
+        }
+        else {
+            return super.estimateRegionsStats(regions, opts);
+        }
+    }
+    freeResources( /* { region } */) { }
     // depends on setup being called before the BAM constructor
-    BamAdapter.prototype.refIdToName = function (refId) {
+    refIdToName(refId) {
         var _a;
         return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];
-    };
-    return BamAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+    }
+}
 exports.default = BamAdapter;
 //# sourceMappingURL=BamAdapter.js.map

package/dist/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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