@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/CramAdapter/CramAdapter.js

@@ -1,259 +1,139 @@
 "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) {
-        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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var cram_1 = require("@gmod/cram");
-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 CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
-var CramAdapter = /** @class */ (function (_super) {
-    __extends(CramAdapter, _super);
-    function CramAdapter() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.samHeader = {};
+const cram_1 = require("@gmod/cram");
+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 CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
+class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.samHeader = {};
         // maps a seqId to original refname, passed specially to render args, to a seqid
-        _this.seqIdToOriginalRefName = [];
-        return _this;
+        this.seqIdToOriginalRefName = [];
     }
-    CramAdapter.prototype.configure = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var cramLocation, craiLocation, cram, sequenceAdapterType, seqConf, sequenceAdapter;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        cramLocation = this.getConf('cramLocation');
-                        craiLocation = this.getConf('craiLocation');
-                        if (!cramLocation) {
-                            throw new Error('missing cramLocation argument');
-                        }
-                        if (!craiLocation) {
-                            throw new Error('missing craiLocation argument');
-                        }
-                        cram = new cram_1.IndexedCramFile({
-                            cramFilehandle: (0, io_1.openLocation)(cramLocation, this.pluginManager),
-                            index: new cram_1.CraiIndex({
-                                filehandle: (0, io_1.openLocation)(craiLocation, this.pluginManager),
-                            }),
-                            seqFetch: this.seqFetch.bind(this),
-                            checkSequenceMD5: false,
-                            fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
-                        });
-                        sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
-                        if (!this.getSubAdapter) {
-                            throw new Error('Error getting subadapter');
-                        }
-                        seqConf = this.getConf('sequenceAdapter');
-                        return [4 /*yield*/, this.getSubAdapter(seqConf)];
-                    case 1:
-                        sequenceAdapter = (_a.sent()).dataAdapter;
-                        if (!(sequenceAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter)) {
-                            throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(sequenceAdapterType, "'"));
-                        }
-                        return [2 /*return*/, { cram: cram, sequenceAdapter: sequenceAdapter }];
-                }
-            });
-        });
-    };
-    CramAdapter.prototype.getHeader = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var cram;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        cram = (_a.sent()).cram;
-                        return [2 /*return*/, cram.cram.getHeaderText(opts)];
-                }
-            });
-        });
-    };
-    CramAdapter.prototype.seqFetch = function (seqId, start, end) {
-        return __awaiter(this, void 0, void 0, function () {
-            var sequenceAdapter, refName, seqChunks, sequence;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        start -= 1; // convert from 1-based closed to interbase
-                        return [4 /*yield*/, this.configure()];
-                    case 1:
-                        sequenceAdapter = (_a.sent()).sequenceAdapter;
-                        refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
-                        if (!refName) {
-                            return [2 /*return*/, undefined];
-                        }
-                        return [4 /*yield*/, sequenceAdapter
-                                .getFeatures({
-                                refName: refName,
-                                start: start,
-                                end: end,
-                                assemblyName: '',
-                            })
-                                .pipe((0, operators_1.toArray)())
-                                .toPromise()];
-                    case 2:
-                        seqChunks = _a.sent();
-                        sequence = seqChunks
-                            .sort(function (a, b) { return a.get('start') - b.get('start'); })
-                            .map(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');
-                            return chunkSeq.substr(trimStart, trimLength);
-                        })
-                            .join('');
-                        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];
-                }
-            });
-        });
-    };
-    CramAdapter.prototype.setupPre = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, statusCallback, configured, cram, samHeader, idToName, nameToId, readGroups, data;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        _a = (opts || {}).statusCallback, statusCallback = _a === void 0 ? function () { } : _a;
-                        return [4 /*yield*/, this.configure()];
-                    case 1:
-                        configured = _b.sent();
-                        statusCallback('Downloading index');
-                        cram = configured.cram;
-                        return [4 /*yield*/, cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal)
-                            // use the @SQ lines in the header to figure out the
-                            // mapping between ref ID numbers and names
-                        ];
-                    case 2:
-                        samHeader = _b.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;
-                                }
-                            });
-                        });
-                        readGroups = samHeader
-                            .filter(function (l) { return l.tag === 'RG'; })
-                            .map(function (rgLine) { var _a; return (_a = rgLine.data.find(function (item) { return item.tag === 'ID'; })) === null || _a === void 0 ? void 0 : _a.value; });
-                        data = { idToName: idToName, nameToId: nameToId, readGroups: readGroups };
-                        statusCallback('');
-                        this.samHeader = data;
-                        return [2 /*return*/, __assign({ samHeader: data }, configured)];
-                }
-            });
+    async configure() {
+        const cramLocation = this.getConf('cramLocation');
+        const craiLocation = this.getConf('craiLocation');
+        if (!cramLocation) {
+            throw new Error('missing cramLocation argument');
+        }
+        if (!craiLocation) {
+            throw new Error('missing craiLocation argument');
+        }
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const cram = new cram_1.IndexedCramFile({
+            cramFilehandle: (0, io_1.openLocation)(cramLocation, this.pluginManager),
+            index: new cram_1.CraiIndex({
+                filehandle: (0, io_1.openLocation)(craiLocation, this.pluginManager),
+            }),
+            seqFetch: this.seqFetch.bind(this),
+            checkSequenceMD5: false,
+            fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
         });
-    };
-    CramAdapter.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;
-                    });
+        // instantiate the sequence adapter
+        const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
+        if (!this.getSubAdapter) {
+            throw new Error('Error getting subadapter');
+        }
+        const seqConf = this.getConf('sequenceAdapter');
+        const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf);
+        if (!(sequenceAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter)) {
+            throw new Error(`CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`);
+        }
+        return { cram, sequenceAdapter };
+    }
+    async getHeader(opts) {
+        const { cram } = await this.configure();
+        return cram.cram.getHeaderText(opts);
+    }
+    async seqFetch(seqId, start, end) {
+        start -= 1; // convert from 1-based closed to interbase
+        const { sequenceAdapter } = await this.configure();
+        const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
+        if (!refName) {
+            return undefined;
+        }
+        const seqChunks = await sequenceAdapter
+            .getFeatures({
+            refName,
+            start,
+            end,
+            assemblyName: '',
+        })
+            .pipe((0, operators_1.toArray)())
+            .toPromise();
+        const sequence = seqChunks
+            .sort((a, b) => a.get('start') - b.get('start'))
+            .map(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');
+            return chunkSeq.substr(trimStart, trimLength);
+        })
+            .join('');
+        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;
+    }
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const configured = await this.configure();
+        statusCallback('Downloading index');
+        const { cram } = configured;
+        const samHeader = await cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+        // use the @SQ lines in the header to figure out the
+        // mapping between 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 [2 /*return*/, this.setupP];
             });
         });
-    };
-    CramAdapter.prototype.getRefNames = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var samHeader;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup(opts)];
-                    case 1:
-                        samHeader = (_a.sent()).samHeader;
-                        if (!samHeader.idToName) {
-                            throw new Error('CRAM file has no header lines');
-                        }
-                        return [2 /*return*/, samHeader.idToName];
-                }
+        const readGroups = samHeader
+            .filter(l => l.tag === 'RG')
+            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
+        const data = { idToName, nameToId, readGroups };
+        statusCallback('');
+        this.samHeader = data;
+        return { samHeader: data, ...configured };
+    }
+    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 { samHeader } = await this.setup(opts);
+        if (!samHeader.idToName) {
+            throw new Error('CRAM file has no header lines');
+        }
+        return samHeader.idToName;
+    }
     // use info from the SAM header if possible, but fall back to using
     // the ref seq order from when the browser's refseqs were loaded
-    CramAdapter.prototype.refNameToId = function (refName) {
+    refNameToId(refName) {
         if (this.samHeader.nameToId) {
             return this.samHeader.nameToId[refName];
         }
@@ -261,10 +141,10 @@ var CramAdapter = /** @class */ (function (_super) {
             return this.seqIdToRefName.indexOf(refName);
         }
         return undefined;
-    };
+    }
     // use info from the SAM header if possible, but fall back to using
     // the ref seq order from when the browser's refseqs were loaded
-    CramAdapter.prototype.refIdToName = function (refId) {
+    refIdToName(refId) {
         if (this.samHeader.idToName) {
             return this.samHeader.idToName[refId];
         }
@@ -272,121 +152,83 @@ var CramAdapter = /** @class */ (function (_super) {
             return this.seqIdToRefName[refId];
         }
         return undefined;
-    };
-    CramAdapter.prototype.refIdToOriginalName = function (refId) {
+    }
+    refIdToOriginalName(refId) {
         return this.seqIdToOriginalRefName[refId];
-    };
-    CramAdapter.prototype.getFeatures = function (region, opts) {
-        var _this = this;
-        var _a = opts || {}, signal = _a.signal, filterBy = _a.filterBy, _b = _a.statusCallback, statusCallback = _b === void 0 ? function () { } : _b;
-        var refName = region.refName, start = region.start, end = region.end, originalRefName = region.originalRefName;
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var _a, cram, sequenceAdapter, _b, refId, records, _c, _d, flagInclude_1, _e, flagExclude_1, tagFilter_1, readName_1, filtered;
-            var _this = this;
-            return __generator(this, function (_f) {
-                switch (_f.label) {
-                    case 0: return [4 /*yield*/, this.setup(opts)];
-                    case 1:
-                        _a = _f.sent(), cram = _a.cram, sequenceAdapter = _a.sequenceAdapter;
-                        statusCallback('Downloading alignments');
-                        if (!!this.seqIdToRefName) return [3 /*break*/, 3];
-                        _b = this;
-                        return [4 /*yield*/, sequenceAdapter.getRefNames(opts)];
-                    case 2:
-                        _b.seqIdToRefName = _f.sent();
-                        _f.label = 3;
-                    case 3:
-                        refId = this.refNameToId(refName);
-                        if (!(refId !== undefined)) return [3 /*break*/, 5];
-                        if (originalRefName) {
-                            this.seqIdToOriginalRefName[refId] = originalRefName;
-                        }
-                        return [4 /*yield*/, cram.getRecordsForRange(refId, start, end, opts)];
-                    case 4:
-                        records = _f.sent();
-                        (0, util_1.checkAbortSignal)(signal);
-                        _c = filterBy || {}, _d = _c.flagInclude, flagInclude_1 = _d === void 0 ? 0 : _d, _e = _c.flagExclude, flagExclude_1 = _e === void 0 ? 0 : _e, tagFilter_1 = _c.tagFilter, readName_1 = _c.readName;
-                        filtered = records.filter(function (record) {
-                            var flags = record.flags;
-                            return (flags & flagInclude_1) === flagInclude_1 && !(flags & flagExclude_1);
-                        });
-                        if (tagFilter_1) {
-                            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                            filtered = filtered.filter(function (record) {
-                                var val = record[tagFilter_1.tag];
-                                return val === '*' ? val !== undefined : val === tagFilter_1.value;
-                            });
-                        }
-                        if (readName_1) {
-                            filtered = filtered.filter(
-                            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                            function (record) { return record.readName === readName_1; });
-                        }
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                        filtered.forEach(function (record) {
-                            observer.next(_this.cramRecordToFeature(record));
-                        });
-                        return [3 /*break*/, 6];
-                    case 5:
-                        console.warn('Unknown refName', refName);
-                        _f.label = 6;
-                    case 6:
-                        statusCallback('');
-                        observer.complete();
-                        return [2 /*return*/];
+    }
+    getFeatures(region, opts) {
+        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { refName, start, end, originalRefName } = region;
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { cram, sequenceAdapter } = await this.setup(opts);
+            statusCallback('Downloading alignments');
+            if (!this.seqIdToRefName) {
+                this.seqIdToRefName = await sequenceAdapter.getRefNames(opts);
+            }
+            const refId = this.refNameToId(refName);
+            if (refId !== undefined) {
+                if (originalRefName) {
+                    this.seqIdToOriginalRefName[refId] = originalRefName;
                 }
-            });
-        }); }, signal);
-    };
-    CramAdapter.prototype.freeResources = function ( /* { region } */) { };
-    CramAdapter.prototype.cramRecordToFeature = function (record) {
+                const records = await cram.getRecordsForRange(refId, start, end, opts);
+                (0, util_1.checkAbortSignal)(signal);
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                let filtered = records.filter((record) => {
+                    const flags = record.flags;
+                    return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
+                });
+                if (tagFilter) {
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    filtered = filtered.filter((record) => {
+                        const val = record[tagFilter.tag];
+                        return val === '*' ? val !== undefined : val === tagFilter.value;
+                    });
+                }
+                if (readName) {
+                    filtered = filtered.filter(
+                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    (record) => record.readName === readName);
+                }
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                filtered.forEach((record) => {
+                    observer.next(this.cramRecordToFeature(record));
+                });
+            }
+            else {
+                console.warn('Unknown refName', refName);
+            }
+            statusCallback('');
+            observer.complete();
+        }, signal);
+    }
+    freeResources( /* { region } */) { }
+    cramRecordToFeature(record) {
         return new CramSlightlyLazyFeature_1.default(record, this);
-    };
+    }
     // we return the configured fetchSizeLimit, and the bytes for the region
-    CramAdapter.prototype.estimateRegionsStats = function (regions, opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var bytes, fetchSizeLimit;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.bytesForRegions(regions, opts)];
-                    case 1:
-                        bytes = _a.sent();
-                        fetchSizeLimit = this.getConf('fetchSizeLimit');
-                        return [2 /*return*/, {
-                                bytes: bytes,
-                                fetchSizeLimit: fetchSizeLimit,
-                            }];
-                }
-            });
-        });
-    };
+    async estimateRegionsStats(regions, opts) {
+        const bytes = await this.bytesForRegions(regions, opts);
+        const fetchSizeLimit = this.getConf('fetchSizeLimit');
+        return {
+            bytes,
+            fetchSizeLimit,
+        };
+    }
     /**
      * get the approximate number of bytes queried from the file for the given
      * query regions
      * @param regions - list of query regions
      */
-    CramAdapter.prototype.bytesForRegions = function (regions, _opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var cram, blockResults;
-            var _this = this;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        cram = (_a.sent()).cram;
-                        return [4 /*yield*/, Promise.all(regions.map(function (region) {
-                                var refName = region.refName, start = region.start, end = region.end;
-                                var chrId = _this.refNameToId(refName);
-                                return cram.index.getEntriesForRange(chrId, start, end);
-                            }))];
-                    case 2:
-                        blockResults = _a.sent();
-                        return [2 /*return*/, blockResults.flat().reduce(function (a, b) { return a + b.sliceBytes; }, 0)];
-                }
-            });
-        });
-    };
-    return CramAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+    async bytesForRegions(regions, _opts) {
+        const { cram } = await this.configure();
+        const blockResults = await Promise.all(regions.map(region => {
+            const { refName, start, end } = region;
+            const chrId = this.refNameToId(refName);
+            return cram.index.getEntriesForRange(chrId, start, end);
+        }));
+        return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
+    }
+}
 exports.default = CramAdapter;
 //# sourceMappingURL=CramAdapter.js.map