@gmod/bam 1.1.17 → 2.0.0

package/dist/htsget.d.ts

@@ -1,7 +1,7 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { BaseOpts, BamOpts } from './util';
 import BamFile from './bamFile';
-import 'cross-fetch/polyfill';
 import Chunk from './chunk';
 export default class HtsgetFile extends BamFile {
     private baseUrl;
@@ -11,16 +11,13 @@ export default class HtsgetFile extends BamFile {
         baseUrl: string;
     });
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record").default[], void, unknown>;
-    _readChunk(params: {
-        chunk: {
-            buffer: Buffer;
-            chunk: Chunk;
-        };
+    _readChunk({ chunk }: {
+        chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
         data: Buffer;
-        cpositions: null;
-        dpositions: null;
+        cpositions: never[];
+        dpositions: never[];
         chunk: Chunk;
     }>;
     getHeader(opts?: BaseOpts): Promise<{

package/dist/htsget.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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -57,33 +31,6 @@ 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 __rest = (this && this.__rest) || function (s, e) {
     var t = {};
     for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
@@ -106,7 +53,7 @@ var __asyncValues = (this && this.__asyncValues) || function (o) {
 var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
     var i, p;
     return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
-    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: n === "return" } : f ? f(v) : v; } : f; }
+    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }
 };
 var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
     if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
@@ -119,171 +66,135 @@ var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _ar
     function reject(value) { resume("throw", value); }
     function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
 };
-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.");
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var bamFile_1 = __importStar(require("./bamFile"));
-require("cross-fetch/polyfill");
-var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-var sam_1 = require("./sam");
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const buffer_1 = require("buffer");
+const bamFile_1 = __importStar(require("./bamFile"));
+const sam_1 = require("./sam");
 function concat(arr, opts) {
-    return __awaiter(this, void 0, void 0, function () {
-        var res, _a, _b;
-        var _this = this;
-        return __generator(this, function (_c) {
-            switch (_c.label) {
-                case 0: return [4 /*yield*/, Promise.all(arr.map(function (chunk) { return __awaiter(_this, void 0, void 0, function () {
-                        var url, headers, referer, rest, res_1, _a, _b;
-                        return __generator(this, function (_c) {
-                            switch (_c.label) {
-                                case 0:
-                                    url = chunk.url, headers = chunk.headers;
-                                    if (!url.startsWith('data:')) return [3 /*break*/, 1];
-                                    return [2 /*return*/, Buffer.from(url.split(',')[1], 'base64')];
-                                case 1:
-                                    referer = headers.referer, rest = __rest(headers, ["referer"]);
-                                    return [4 /*yield*/, fetch(url, __assign(__assign({}, opts), { headers: __assign(__assign({}, opts.headers), rest) }))];
-                                case 2:
-                                    res_1 = _c.sent();
-                                    if (!res_1.ok) {
-                                        throw new Error("Failed to fetch ".concat(res_1.statusText));
-                                    }
-                                    _b = (_a = Buffer).from;
-                                    return [4 /*yield*/, res_1.arrayBuffer()];
-                                case 3: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
-                            }
-                        });
-                    }); }))];
-                case 1:
-                    res = _c.sent();
-                    _b = (_a = Buffer).concat;
-                    return [4 /*yield*/, Promise.all(res.map(function (elt) { return (0, bgzf_filehandle_1.unzip)(elt); }))];
-                case 2: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
+    return __awaiter(this, void 0, void 0, function* () {
+        const res = yield Promise.all(arr.map((chunk) => __awaiter(this, void 0, void 0, function* () {
+            const { url, headers } = chunk;
+            if (url.startsWith('data:')) {
+                return buffer_1.Buffer.from(url.split(',')[1], 'base64');
             }
-        });
+            else {
+                //remove referer header, it is not even allowed to be specified
+                // @ts-expect-error
+                //eslint-disable-next-line @typescript-eslint/no-unused-vars
+                const { referer } = headers, rest = __rest(headers, ["referer"]);
+                const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, opts === null || opts === void 0 ? void 0 : opts.headers), rest) }));
+                if (!res.ok) {
+                    throw new Error(`HTTP ${res.status} fetching ${url}: ${yield res.text()}`);
+                }
+                return buffer_1.Buffer.from(yield res.arrayBuffer());
+            }
+        })));
+        return buffer_1.Buffer.concat(yield Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
     });
 }
-var HtsgetFile = /** @class */ (function (_super) {
-    __extends(HtsgetFile, _super);
-    function HtsgetFile(args) {
-        var _this = 
-        // @ts-ignore override bam defaults
-        _super.call(this, { bamFilehandle: '?', baiFilehandle: '?' }) || this;
-        _this.baseUrl = args.baseUrl;
-        _this.trackId = args.trackId;
-        return _this;
+class HtsgetFile extends bamFile_1.default {
+    constructor(args) {
+        super({ htsget: true });
+        this.baseUrl = args.baseUrl;
+        this.trackId = args.trackId;
     }
-    HtsgetFile.prototype.streamRecordsForRange = function (chr, min, max, opts) {
-        if (opts === void 0) { opts = {
-            viewAsPairs: false,
-            pairAcrossChr: false,
-            maxInsertSize: 200000,
-        }; }
-        return __asyncGenerator(this, arguments, function streamRecordsForRange_1() {
-            var base, url, chrId, result, data, uncba, chunk;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        base = "".concat(this.baseUrl, "/").concat(this.trackId);
-                        url = "".concat(base, "?referenceName=").concat(chr, "&start=").concat(min, "&end=").concat(max, "&format=BAM");
-                        chrId = this.chrToIndex && this.chrToIndex[chr];
-                        return [4 /*yield*/, __await(fetch(url, __assign({}, opts)))];
-                    case 1:
-                        result = _a.sent();
-                        if (!result.ok) {
-                            throw new Error(result.statusText);
-                        }
-                        return [4 /*yield*/, __await(result.json())];
-                    case 2:
-                        data = _a.sent();
-                        return [4 /*yield*/, __await(concat(data.htsget.urls.slice(1), opts))];
-                    case 3:
-                        uncba = _a.sent();
-                        chunk = {
-                            buffer: uncba,
-                            chunk: { minv: { dataPosition: 0 } },
-                            toString: function () {
-                                return "".concat(chr, "_").concat(min, "_").concat(max);
-                            },
-                        };
-                        return [5 /*yield**/, __values(__asyncDelegator(__asyncValues(this._fetchChunkFeatures(
-                            // @ts-ignore
-                            [chunk], chrId, min, max, opts))))];
-                    case 4: return [4 /*yield*/, __await.apply(void 0, [_a.sent()])];
-                    case 5:
-                        _a.sent();
-                        return [2 /*return*/];
+    streamRecordsForRange(chr, min, max, opts) {
+        var _a;
+        return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
+            const base = `${this.baseUrl}/${this.trackId}`;
+            const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
+            const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
+            if (chrId === undefined) {
+                yield yield __await([]);
+            }
+            else {
+                const result = yield __await(fetch(url, Object.assign({}, opts)));
+                if (!result.ok) {
+                    throw new Error(`HTTP ${result.status} fetching ${url}: ${yield __await(result.text())}`);
                 }
-            });
+                const data = yield __await(result.json());
+                const uncba = yield __await(concat(data.htsget.urls.slice(1), opts));
+                yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures([
+                    // fake stuff to pretend to be a Chunk
+                    {
+                        buffer: uncba,
+                        _fetchedSize: undefined,
+                        bin: 0,
+                        compareTo() {
+                            return 0;
+                        },
+                        toUniqueString() {
+                            return `${chr}_${min}_${max}`;
+                        },
+                        fetchedSize() {
+                            return 0;
+                        },
+                        minv: {
+                            dataPosition: 0,
+                            blockPosition: 0,
+                            compareTo: () => 0,
+                        },
+                        maxv: {
+                            dataPosition: Number.MAX_SAFE_INTEGER,
+                            blockPosition: 0,
+                            compareTo: () => 0,
+                        },
+                        toString() {
+                            return `${chr}_${min}_${max}`;
+                        },
+                    },
+                ], chrId, min, max, opts))));
+            }
         });
-    };
-    //@ts-ignore
-    HtsgetFile.prototype._readChunk = function (params) {
-        return __awaiter(this, void 0, void 0, function () {
-            var chunk, buffer, c2;
-            return __generator(this, function (_a) {
-                chunk = params.chunk;
-                buffer = chunk.buffer, c2 = chunk.chunk;
-                return [2 /*return*/, { data: buffer, cpositions: null, dpositions: null, chunk: c2 }];
-            });
+    }
+    _readChunk({ chunk }) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!chunk.buffer) {
+                throw new Error('expected chunk.buffer in htsget');
+            }
+            return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
         });
-    };
-    HtsgetFile.prototype.getHeader = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var url, result, data, uncba, headLen, headerText, samHeader, idToName, nameToId, sqLines;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        url = "".concat(this.baseUrl, "/").concat(this.trackId, "?referenceName=na&class=header");
-                        return [4 /*yield*/, fetch(url, opts)];
-                    case 1:
-                        result = _a.sent();
-                        if (!result.ok) {
-                            throw new Error("Failed to fetch ".concat(result.statusText));
-                        }
-                        return [4 /*yield*/, result.json()];
-                    case 2:
-                        data = _a.sent();
-                        return [4 /*yield*/, concat(data.htsget.urls, opts)];
-                    case 3:
-                        uncba = _a.sent();
-                        if (uncba.readInt32LE(0) !== bamFile_1.BAM_MAGIC) {
-                            throw new Error('Not a BAM file');
-                        }
-                        headLen = uncba.readInt32LE(4);
-                        headerText = uncba.toString('utf8', 8, 8 + headLen);
-                        samHeader = (0, sam_1.parseHeaderText)(headerText);
-                        idToName = [];
-                        nameToId = {};
-                        sqLines = samHeader.filter(function (l) { return l.tag === 'SQ'; });
-                        sqLines.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;
-                                }
-                            });
-                        });
-                        this.chrToIndex = nameToId;
-                        this.indexToChr = idToName;
-                        return [2 /*return*/, samHeader];
+    }
+    getHeader(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
+            const result = yield fetch(url, opts);
+            if (!result.ok) {
+                throw new Error(`HTTP ${result.status} fetching ${url}: ${yield result.text()}`);
+            }
+            const data = yield result.json();
+            const uncba = yield concat(data.htsget.urls, opts);
+            if (uncba.readInt32LE(0) !== bamFile_1.BAM_MAGIC) {
+                throw new Error('Not a BAM file');
+            }
+            const headLen = uncba.readInt32LE(4);
+            const headerText = uncba.toString('utf8', 8, 8 + headLen);
+            const samHeader = (0, sam_1.parseHeaderText)(headerText);
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ref ID numbers and names
+            const idToName = [];
+            const nameToId = {};
+            const sqLines = samHeader.filter(l => l.tag === 'SQ');
+            for (const [refId, sqLine] of sqLines.entries()) {
+                let refName = '';
+                let length = 0;
+                for (const item of sqLine.data) {
+                    if (item.tag === 'SN') {
+                        refName = item.value;
+                    }
+                    else if (item.tag === 'LN') {
+                        length = +item.value;
+                    }
                 }
-            });
+                nameToId[refName] = refId;
+                idToName[refId] = { refName, length };
+            }
+            this.chrToIndex = nameToId;
+            this.indexToChr = idToName;
+            return samHeader;
         });
-    };
-    return HtsgetFile;
-}(bamFile_1.default));
+    }
+}
 exports.default = HtsgetFile;
 //# sourceMappingURL=htsget.js.map

package/dist/htsget.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,6 +1,5 @@
-import BAI from './bai';
-import CSI from './csi';
-import BamFile from './bamFile';
-import HtsgetFile from './htsget';
-import BamRecord from './record';
-export { BAI, CSI, BamFile, BamRecord, HtsgetFile };
+export { default as BAI } from './bai';
+export { default as BamFile } from './bamFile';
+export { default as CSI } from './csi';
+export { default as BamRecord } from './record';
+export { default as HtsgetFile } from './htsget';

package/dist/index.js

@@ -3,15 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.HtsgetFile = exports.BamRecord = exports.BamFile = exports.CSI = exports.BAI = void 0;
-var bai_1 = __importDefault(require("./bai"));
-exports.BAI = bai_1.default;
-var csi_1 = __importDefault(require("./csi"));
-exports.CSI = csi_1.default;
-var bamFile_1 = __importDefault(require("./bamFile"));
-exports.BamFile = bamFile_1.default;
-var htsget_1 = __importDefault(require("./htsget"));
-exports.HtsgetFile = htsget_1.default;
-var record_1 = __importDefault(require("./record"));
-exports.BamRecord = record_1.default;
+exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.BAI = void 0;
+var bai_1 = require("./bai");
+Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_1).default; } });
+var bamFile_1 = require("./bamFile");
+Object.defineProperty(exports, "BamFile", { enumerable: true, get: function () { return __importDefault(bamFile_1).default; } });
+var csi_1 = require("./csi");
+Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_1).default; } });
+var record_1 = require("./record");
+Object.defineProperty(exports, "BamRecord", { enumerable: true, get: function () { return __importDefault(record_1).default; } });
+var htsget_1 = require("./htsget");
+Object.defineProperty(exports, "HtsgetFile", { enumerable: true, get: function () { return __importDefault(htsget_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAuB;AAMd,cANF,aAAG,CAME;AALZ,8CAAuB;AAKT,cALP,aAAG,CAKO;AAJjB,sDAA+B;AAIZ,kBAJZ,iBAAO,CAIY;AAH1B,oDAAiC;AAGM,qBAHhC,gBAAU,CAGgC;AAFjD,oDAAgC;AAEJ,oBAFrB,gBAAS,CAEqB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,6BAAsC;AAA7B,2GAAA,OAAO,OAAO;AACvB,qCAA8C;AAArC,mHAAA,OAAO,OAAW;AAC3B,6BAAsC;AAA7B,2GAAA,OAAO,OAAO;AACvB,mCAA+C;AAAtC,oHAAA,OAAO,OAAa;AAC7B,mCAAgD;AAAvC,qHAAA,OAAO,OAAc"}

package/dist/indexFile.d.ts

@@ -1,11 +1,9 @@
 import { GenericFilehandle } from 'generic-filehandle';
-import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    setupP?: Promise<any>;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]
@@ -15,14 +13,10 @@ export default abstract class IndexFile {
         renameRefSeq?: (a: string) => string;
     });
     abstract lineCount(refId: number): Promise<number>;
-    protected abstract _parse(opts?: BaseOpts): Promise<any>;
     abstract indexCov(refId: number, start?: number, end?: number): Promise<{
         start: number;
         end: number;
         score: number;
     }[]>;
     abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
-    _findFirstData(data: any, virtualOffset: VirtualOffset): void;
-    parse(opts?: BaseOpts): Promise<any>;
-    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }

package/dist/indexFile.js

@@ -1,88 +1,14 @@
 "use strict";
-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 };
-    }
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var IndexFile = /** @class */ (function () {
+class IndexFile {
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]
      */
-    function IndexFile(_a) {
-        var filehandle = _a.filehandle, _b = _a.renameRefSeq, renameRefSeq = _b === void 0 ? function (n) { return n; } : _b;
+    constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
     }
-    IndexFile.prototype._findFirstData = function (data, virtualOffset) {
-        var currentFdl = data.firstDataLine;
-        if (currentFdl) {
-            data.firstDataLine =
-                currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-        }
-        else {
-            data.firstDataLine = virtualOffset;
-        }
-    };
-    IndexFile.prototype.parse = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.setupP) {
-                    this.setupP = this._parse(opts).catch(function (e) {
-                        _this.setupP = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.setupP];
-            });
-        });
-    };
-    IndexFile.prototype.hasRefSeq = function (seqId, opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.parse(opts)];
-                    case 1: return [2 /*return*/, !!((_a.sent()).indices[seqId] || {}).binIndex];
-                }
-            });
-        });
-    };
-    return IndexFile;
-}());
+}
 exports.default = IndexFile;
 //# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAIA,MAA8B,SAAS;IAIrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF;AA/BD,4BA+BC"}

package/dist/nullIndex.d.ts

@@ -0,0 +1,7 @@
+import IndexFile from './indexFile';
+export default class NullIndex extends IndexFile {
+    lineCount(): Promise<any>;
+    protected _parse(): Promise<any>;
+    indexCov(): Promise<any>;
+    blocksForRange(): Promise<any>;
+}