@gmod/bam 4.0.1 → 5.0.0

package/dist/bamFile.js

@@ -1,47 +1,12 @@
 "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 __asyncValues = (this && this.__asyncValues) || function (o) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var m = o[Symbol.asyncIterator], i;
-    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
-    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
-    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
-};
-var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-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: 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.");
-    var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = Object.create((typeof AsyncIterator === "function" ? AsyncIterator : Object).prototype), verb("next"), verb("throw"), verb("return", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }
-    function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }
-    function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
-    function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
-    function fulfill(value) { resume("next", value); }
-    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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BAM_MAGIC = void 0;
-const buffer_1 = require("buffer");
 const crc32_1 = __importDefault(require("crc/crc32"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 // locals
@@ -52,28 +17,12 @@ const sam_1 = require("./sam");
 const util_1 = require("./util");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
-function gen2array(gen) {
-    return __awaiter(this, void 0, void 0, function* () {
-        var _a, gen_1, gen_1_1;
-        var _b, e_1, _c, _d;
-        let out = [];
-        try {
-            for (_a = true, gen_1 = __asyncValues(gen); gen_1_1 = yield gen_1.next(), _b = gen_1_1.done, !_b; _a = true) {
-                _d = gen_1_1.value;
-                _a = false;
-                const x = _d;
-                out = out.concat(x);
-            }
-        }
-        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-        finally {
-            try {
-                if (!_a && !_b && (_c = gen_1.return)) yield _c.call(gen_1);
-            }
-            finally { if (e_1) throw e_1.error; }
-        }
-        return out;
-    });
+async function gen2array(gen) {
+    let out = [];
+    for await (const x of gen) {
+        out = out.concat(x);
+    }
+    return out;
 }
 class NullFilehandle {
     read() {
@@ -90,30 +39,38 @@ class NullFilehandle {
     }
 }
 class BamFile {
+    renameRefSeq;
+    bam;
+    header;
+    chrToIndex;
+    indexToChr;
+    yieldThreadTime;
+    index;
+    htsget = false;
+    headerP;
+    featureCache = new abortable_promise_cache_1.default({
+        cache: new quick_lru_1.default({
+            maxSize: 50,
+        }),
+        fill: async (args, signal) => {
+            const { chunk, opts } = args;
+            const { data, cpositions, dpositions } = await this._readChunk({
+                chunk,
+                opts: { ...opts, signal },
+            });
+            return this.readBamFeatures(data, cpositions, dpositions, chunk);
+        },
+    });
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
-        this.htsget = false;
-        this.featureCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({
-                maxSize: 50,
-            }),
-            fill: (args, signal) => __awaiter(this, void 0, void 0, function* () {
-                const { chunk, opts } = args;
-                const { data, cpositions, dpositions } = yield this._readChunk({
-                    chunk,
-                    opts: Object.assign(Object.assign({}, opts), { signal }),
-                });
-                return this.readBamFeatures(data, cpositions, dpositions, chunk);
-            }),
-        });
         this.renameRefSeq = renameRefSeqs;
         if (bamFilehandle) {
             this.bam = bamFilehandle;
         }
         else if (bamPath) {
-            this.bam = new generic_filehandle_1.LocalFile(bamPath);
+            this.bam = new generic_filehandle2_1.LocalFile(bamPath);
         }
         else if (bamUrl) {
-            this.bam = new generic_filehandle_1.RemoteFile(bamUrl);
+            this.bam = new generic_filehandle2_1.RemoteFile(bamUrl);
         }
         else if (htsget) {
             this.htsget = true;
@@ -126,25 +83,25 @@ class BamFile {
             this.index = new csi_1.default({ filehandle: csiFilehandle });
         }
         else if (csiPath) {
-            this.index = new csi_1.default({ filehandle: new generic_filehandle_1.LocalFile(csiPath) });
+            this.index = new csi_1.default({ filehandle: new generic_filehandle2_1.LocalFile(csiPath) });
         }
         else if (csiUrl) {
-            this.index = new csi_1.default({ filehandle: new generic_filehandle_1.RemoteFile(csiUrl) });
+            this.index = new csi_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(csiUrl) });
         }
         else if (baiFilehandle) {
             this.index = new bai_1.default({ filehandle: baiFilehandle });
         }
         else if (baiPath) {
-            this.index = new bai_1.default({ filehandle: new generic_filehandle_1.LocalFile(baiPath) });
+            this.index = new bai_1.default({ filehandle: new generic_filehandle2_1.LocalFile(baiPath) });
         }
         else if (baiUrl) {
-            this.index = new bai_1.default({ filehandle: new generic_filehandle_1.RemoteFile(baiUrl) });
+            this.index = new bai_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(baiUrl) });
         }
         else if (bamPath) {
-            this.index = new bai_1.default({ filehandle: new generic_filehandle_1.LocalFile(`${bamPath}.bai`) });
+            this.index = new bai_1.default({ filehandle: new generic_filehandle2_1.LocalFile(`${bamPath}.bai`) });
         }
         else if (bamUrl) {
-            this.index = new bai_1.default({ filehandle: new generic_filehandle_1.RemoteFile(`${bamUrl}.bai`) });
+            this.index = new bai_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(`${bamUrl}.bai`) });
         }
         else if (htsget) {
             this.htsget = true;
@@ -154,39 +111,35 @@ class BamFile {
         }
         this.yieldThreadTime = yieldThreadTime;
     }
-    getHeaderPre(origOpts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const opts = (0, util_1.makeOpts)(origOpts);
-            if (!this.index) {
-                return;
-            }
-            const indexData = yield this.index.parse(opts);
-            const ret = indexData.firstDataLine
-                ? indexData.firstDataLine.blockPosition + 65535
-                : undefined;
-            let buffer;
-            if (ret) {
-                const s = ret + blockLen;
-                const res = yield this.bam.read(buffer_1.Buffer.alloc(s), 0, s, 0, opts);
-                if (!res.bytesRead) {
-                    throw new Error('Error reading header');
-                }
-                buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
-            }
-            else {
-                buffer = yield this.bam.readFile(opts);
-            }
-            const uncba = yield (0, bgzf_filehandle_1.unzip)(buffer);
-            if (uncba.readInt32LE(0) !== exports.BAM_MAGIC) {
-                throw new Error('Not a BAM file');
-            }
-            const headLen = uncba.readInt32LE(4);
-            this.header = uncba.toString('utf8', 8, 8 + headLen);
-            const { chrToIndex, indexToChr } = yield this._readRefSeqs(headLen + 8, 65535, opts);
-            this.chrToIndex = chrToIndex;
-            this.indexToChr = indexToChr;
-            return (0, sam_1.parseHeaderText)(this.header);
-        });
+    async getHeaderPre(origOpts) {
+        const opts = (0, util_1.makeOpts)(origOpts);
+        if (!this.index) {
+            return;
+        }
+        const indexData = await this.index.parse(opts);
+        const ret = indexData.firstDataLine
+            ? indexData.firstDataLine.blockPosition + 65535
+            : undefined;
+        let buffer;
+        if (ret) {
+            const s = ret + blockLen;
+            buffer = await this.bam.read(s, 0);
+        }
+        else {
+            buffer = await this.bam.readFile(opts);
+        }
+        const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+        const dataView = new DataView(uncba.buffer);
+        if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
+            throw new Error('Not a BAM file');
+        }
+        const headLen = dataView.getInt32(4, true);
+        const decoder = new TextDecoder('utf8');
+        this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
+        const { chrToIndex, indexToChr } = await this._readRefSeqs(headLen + 8, 65535, opts);
+        this.chrToIndex = chrToIndex;
+        this.indexToChr = indexToChr;
+        return (0, sam_1.parseHeaderText)(this.header);
     }
     getHeader(opts) {
         if (!this.headerP) {
@@ -197,271 +150,239 @@ class BamFile {
         }
         return this.headerP;
     }
-    getHeaderText() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            yield this.getHeader(opts);
-            return this.header;
-        });
+    async getHeaderText(opts = {}) {
+        await this.getHeader(opts);
+        return this.header;
     }
     // the full length of the refseq block is not given in advance so this grabs
     // a chunk and doubles it if all refseqs haven't been processed
-    _readRefSeqs(start, refSeqBytes, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (start > refSeqBytes) {
+    async _readRefSeqs(start, refSeqBytes, opts) {
+        if (start > refSeqBytes) {
+            return this._readRefSeqs(start, refSeqBytes * 2, opts);
+        }
+        // const size = refSeqBytes + blockLen <-- use this?
+        const buffer = await this.bam.read(refSeqBytes, 0, opts);
+        const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+        const dataView = new DataView(uncba.buffer);
+        const nRef = dataView.getInt32(start, true);
+        let p = start + 4;
+        const chrToIndex = {};
+        const indexToChr = [];
+        const decoder = new TextDecoder('utf8');
+        for (let i = 0; i < nRef; i += 1) {
+            const lName = dataView.getInt32(p, true);
+            const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
+            const lRef = dataView.getInt32(p + lName + 4, true);
+            chrToIndex[refName] = i;
+            indexToChr.push({ refName, length: lRef });
+            p = p + 8 + lName;
+            if (p > uncba.length) {
+                console.warn(`BAM header is very big.  Re-fetching ${refSeqBytes} bytes.`);
                 return this._readRefSeqs(start, refSeqBytes * 2, opts);
             }
-            const size = refSeqBytes + blockLen;
-            const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, refSeqBytes, 0, opts);
-            if (!bytesRead) {
-                throw new Error('Error reading refseqs from header');
-            }
-            const uncba = yield (0, bgzf_filehandle_1.unzip)(buffer.subarray(0, Math.min(bytesRead, refSeqBytes)));
-            const nRef = uncba.readInt32LE(start);
-            let p = start + 4;
-            const chrToIndex = {};
-            const indexToChr = [];
-            for (let i = 0; i < nRef; i += 1) {
-                const lName = uncba.readInt32LE(p);
-                const refName = this.renameRefSeq(uncba.toString('utf8', p + 4, p + 4 + lName - 1));
-                const lRef = uncba.readInt32LE(p + lName + 4);
-                chrToIndex[refName] = i;
-                indexToChr.push({ refName, length: lRef });
-                p = p + 8 + lName;
-                if (p > uncba.length) {
-                    console.warn(`BAM header is very big.  Re-fetching ${refSeqBytes} bytes.`);
-                    return this._readRefSeqs(start, refSeqBytes * 2, opts);
-                }
-            }
-            return { chrToIndex, indexToChr };
-        });
+        }
+        return { chrToIndex, indexToChr };
     }
-    getRecordsForRange(chr, min, max, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return gen2array(this.streamRecordsForRange(chr, min, max, opts));
-        });
+    async getRecordsForRange(chr, min, max, opts) {
+        return gen2array(this.streamRecordsForRange(chr, min, max, opts));
     }
-    streamRecordsForRange(chr, min, max, opts) {
-        return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
-            var _a;
-            yield __await(this.getHeader(opts));
-            const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
-            if (chrId === undefined || !this.index) {
-                yield yield __await([]);
-            }
-            else {
-                const chunks = yield __await(this.index.blocksForRange(chrId, min - 1, max, opts));
-                yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures(chunks, chrId, min, max, opts))));
-            }
-        });
+    async *streamRecordsForRange(chr, min, max, opts) {
+        await this.getHeader(opts);
+        const chrId = this.chrToIndex?.[chr];
+        if (chrId === undefined || !this.index) {
+            yield [];
+        }
+        else {
+            const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
+            yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
+        }
     }
-    _fetchChunkFeatures(chunks_1, chrId_1, min_1, max_1) {
-        return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1(chunks, chrId, min, max, opts = {}) {
-            const { viewAsPairs } = opts;
-            const feats = [];
-            let done = false;
-            for (const chunk of chunks) {
-                const records = yield __await(this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal));
-                const recs = [];
-                for (const feature of records) {
-                    if (feature.ref_id === chrId) {
-                        if (feature.start >= max) {
-                            // past end of range, can stop iterating
-                            done = true;
-                            break;
-                        }
-                        else if (feature.end >= min) {
-                            // must be in range
-                            recs.push(feature);
-                        }
+    async *_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
+        const { viewAsPairs } = opts;
+        const feats = [];
+        let done = false;
+        for (const chunk of chunks) {
+            const records = await this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal);
+            const recs = [];
+            for (const feature of records) {
+                if (feature.ref_id === chrId) {
+                    if (feature.start >= max) {
+                        // past end of range, can stop iterating
+                        done = true;
+                        break;
+                    }
+                    else if (feature.end >= min) {
+                        // must be in range
+                        recs.push(feature);
                     }
-                }
-                feats.push(recs);
-                yield yield __await(recs);
-                if (done) {
-                    break;
                 }
             }
-            (0, util_1.checkAbortSignal)(opts.signal);
-            if (viewAsPairs) {
-                yield yield __await(this.fetchPairs(chrId, feats, opts));
+            feats.push(recs);
+            yield recs;
+            if (done) {
+                break;
             }
-        });
+        }
+        (0, util_1.checkAbortSignal)(opts.signal);
+        if (viewAsPairs) {
+            yield this.fetchPairs(chrId, feats, opts);
+        }
     }
-    fetchPairs(chrId, feats, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { pairAcrossChr, maxInsertSize = 200000 } = opts;
-            const unmatedPairs = {};
-            const readIds = {};
-            feats.map(ret => {
-                const readNames = {};
-                for (const element of ret) {
-                    const name = element.name;
-                    const id = element.id;
-                    if (!readNames[name]) {
-                        readNames[name] = 0;
-                    }
-                    readNames[name]++;
-                    readIds[id] = 1;
+    async fetchPairs(chrId, feats, opts) {
+        const { pairAcrossChr, maxInsertSize = 200000 } = opts;
+        const unmatedPairs = {};
+        const readIds = {};
+        feats.map(ret => {
+            const readNames = {};
+            for (const element of ret) {
+                const name = element.name;
+                const id = element.id;
+                if (!readNames[name]) {
+                    readNames[name] = 0;
                 }
-                for (const [k, v] of Object.entries(readNames)) {
-                    if (v === 1) {
-                        unmatedPairs[k] = true;
-                    }
+                readNames[name]++;
+                readIds[id] = 1;
+            }
+            for (const [k, v] of Object.entries(readNames)) {
+                if (v === 1) {
+                    unmatedPairs[k] = true;
                 }
-            });
-            const matePromises = [];
-            feats.map(ret => {
-                for (const f of ret) {
-                    const name = f.name;
-                    const start = f.start;
-                    const pnext = f.next_pos;
-                    const rnext = f.next_refid;
-                    if (this.index &&
-                        unmatedPairs[name] &&
-                        (pairAcrossChr ||
-                            (rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
-                        matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
-                    }
+            }
+        });
+        const matePromises = [];
+        feats.map(ret => {
+            for (const f of ret) {
+                const name = f.name;
+                const start = f.start;
+                const pnext = f.next_pos;
+                const rnext = f.next_refid;
+                if (this.index &&
+                    unmatedPairs[name] &&
+                    (pairAcrossChr ||
+                        (rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
+                    matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
                 }
+            }
+        });
+        // filter out duplicate chunks (the blocks are lists of chunks, blocks are
+        // concatenated, then filter dup chunks)
+        const map = new Map();
+        const res = await Promise.all(matePromises);
+        for (const m of res.flat()) {
+            if (!map.has(m.toString())) {
+                map.set(m.toString(), m);
+            }
+        }
+        const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
+            const { data, cpositions, dpositions, chunk } = await this._readChunk({
+                chunk: c,
+                opts,
             });
-            // filter out duplicate chunks (the blocks are lists of chunks, blocks are
-            // concatenated, then filter dup chunks)
-            const map = new Map();
-            const res = yield Promise.all(matePromises);
-            for (const m of res.flat()) {
-                if (!map.has(m.toString())) {
-                    map.set(m.toString(), m);
+            const mateRecs = [];
+            for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
+                if (unmatedPairs[feature.name] && !readIds[feature.id]) {
+                    mateRecs.push(feature);
                 }
             }
-            const mateFeatPromises = yield Promise.all([...map.values()].map((c) => __awaiter(this, void 0, void 0, function* () {
-                const { data, cpositions, dpositions, chunk } = yield this._readChunk({
-                    chunk: c,
-                    opts,
-                });
-                const mateRecs = [];
-                for (const feature of yield this.readBamFeatures(data, cpositions, dpositions, chunk)) {
-                    if (unmatedPairs[feature.name] && !readIds[feature.id]) {
-                        mateRecs.push(feature);
-                    }
-                }
-                return mateRecs;
-            })));
-            return mateFeatPromises.flat();
-        });
+            return mateRecs;
+        }));
+        return mateFeatPromises.flat();
     }
-    _readRegion(position_1, size_1) {
-        return __awaiter(this, arguments, void 0, function* (position, size, opts = {}) {
-            const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, size, position, opts);
-            return buffer.subarray(0, Math.min(bytesRead, size));
-        });
+    async _readRegion(position, size, opts = {}) {
+        return this.bam.read(size, position, opts);
     }
-    _readChunk(_a) {
-        return __awaiter(this, arguments, void 0, function* ({ chunk, opts }) {
-            const buffer = yield this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
-            const { buffer: data, cpositions, dpositions, } = yield (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
-            return { data, cpositions, dpositions, chunk };
-        });
+    async _readChunk({ chunk, opts }) {
+        const buffer = await this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
+        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
+        return { data, cpositions, dpositions, chunk };
     }
-    readBamFeatures(ba, cpositions, dpositions, chunk) {
-        return __awaiter(this, void 0, void 0, function* () {
-            let blockStart = 0;
-            const sink = [];
-            let pos = 0;
-            let last = +Date.now();
-            while (blockStart + 4 < ba.length) {
-                const blockSize = ba.readInt32LE(blockStart);
-                const blockEnd = blockStart + 4 + blockSize - 1;
-                // increment position to the current decompressed status
-                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                if (dpositions) {
-                    while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
-                    pos--;
-                }
-                // only try to read the feature if we have all the bytes for it
-                if (blockEnd < ba.length) {
-                    const feature = new record_1.default({
-                        bytes: {
-                            byteArray: ba,
-                            start: blockStart,
-                            end: blockEnd,
-                        },
-                        // the below results in an automatically calculated file-offset based
-                        // ID if the info for that is available, otherwise crc32 of the
-                        // features
-                        //
-                        // cpositions[pos] refers to actual file offset of a bgzip block
-                        // boundaries
-                        //
-                        // we multiply by (1 <<8) in order to make sure each block has a
-                        // "unique" address space so that data in that block could never
-                        // overlap
-                        //
-                        // then the blockStart-dpositions is an uncompressed file offset from
-                        // that bgzip block boundary, and since the cpositions are multiplied
-                        // by (1 << 8) these uncompressed offsets get a unique space
-                        //
-                        // this has an extra chunk.minv.dataPosition added on because it
-                        // blockStart starts at 0 instead of chunk.minv.dataPosition
-                        //
-                        // the +1 is just to avoid any possible uniqueId 0 but this does not
-                        // realistically happen
-                        fileOffset: cpositions.length > 0
-                            ? cpositions[pos] * (1 << 8) +
-                                (blockStart - dpositions[pos]) +
-                                chunk.minv.dataPosition +
-                                1
-                            : // must be slice, not subarray for buffer polyfill on web
-                                // eslint-disable-next-line @typescript-eslint/no-deprecated
-                                crc32_1.default.signed(ba.slice(blockStart, blockEnd)),
-                    });
-                    sink.push(feature);
-                    if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
-                        yield (0, util_1.timeout)(1);
-                        last = +Date.now();
-                    }
+    async readBamFeatures(ba, cpositions, dpositions, chunk) {
+        let blockStart = 0;
+        const sink = [];
+        let pos = 0;
+        let last = +Date.now();
+        const dataView = new DataView(ba.buffer);
+        while (blockStart + 4 < ba.length) {
+            const blockSize = dataView.getInt32(blockStart, true);
+            const blockEnd = blockStart + 4 + blockSize - 1;
+            // increment position to the current decompressed status
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            if (dpositions) {
+                while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
+                pos--;
+            }
+            // only try to read the feature if we have all the bytes for it
+            if (blockEnd < ba.length) {
+                const feature = new record_1.default({
+                    bytes: {
+                        byteArray: ba,
+                        start: blockStart,
+                        end: blockEnd,
+                    },
+                    // the below results in an automatically calculated file-offset based
+                    // ID if the info for that is available, otherwise crc32 of the
+                    // features
+                    //
+                    // cpositions[pos] refers to actual file offset of a bgzip block
+                    // boundaries
+                    //
+                    // we multiply by (1 <<8) in order to make sure each block has a
+                    // "unique" address space so that data in that block could never
+                    // overlap
+                    //
+                    // then the blockStart-dpositions is an uncompressed file offset from
+                    // that bgzip block boundary, and since the cpositions are multiplied
+                    // by (1 << 8) these uncompressed offsets get a unique space
+                    //
+                    // this has an extra chunk.minv.dataPosition added on because it
+                    // blockStart starts at 0 instead of chunk.minv.dataPosition
+                    //
+                    // the +1 is just to avoid any possible uniqueId 0 but this does not
+                    // realistically happen
+                    fileOffset: cpositions.length > 0
+                        ? cpositions[pos] * (1 << 8) +
+                            (blockStart - dpositions[pos]) +
+                            chunk.minv.dataPosition +
+                            1
+                        : // must be slice, not subarray for buffer polyfill on web
+                            // @ts-expect-error
+                            crc32_1.default.signed(ba.subarray(blockStart, blockEnd)),
+                });
+                sink.push(feature);
+                if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
+                    await (0, util_1.timeout)(1);
+                    last = +Date.now();
                 }
-                blockStart = blockEnd + 1;
             }
-            return sink;
-        });
+            blockStart = blockEnd + 1;
+        }
+        return sink;
     }
-    hasRefSeq(seqName) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
-            return seqId === undefined ? false : (_b = this.index) === null || _b === void 0 ? void 0 : _b.hasRefSeq(seqId);
-        });
+    async hasRefSeq(seqName) {
+        const seqId = this.chrToIndex?.[seqName];
+        return seqId === undefined ? false : this.index?.hasRefSeq(seqId);
     }
-    lineCount(seqName) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
-            return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
-        });
+    async lineCount(seqName) {
+        const seqId = this.chrToIndex?.[seqName];
+        return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
     }
-    indexCov(seqName, start, end) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            if (!this.index) {
-                return [];
-            }
-            yield this.index.parse();
-            const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
-            return seqId === undefined ? [] : this.index.indexCov(seqId, start, end);
-        });
+    async indexCov(seqName, start, end) {
+        if (!this.index) {
+            return [];
+        }
+        await this.index.parse();
+        const seqId = this.chrToIndex?.[seqName];
+        return seqId === undefined ? [] : this.index.indexCov(seqId, start, end);
     }
-    blocksForRange(seqName, start, end, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            if (!this.index) {
-                return [];
-            }
-            yield this.index.parse();
-            const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
-            return seqId === undefined
-                ? []
-                : this.index.blocksForRange(seqId, start, end, opts);
-        });
+    async blocksForRange(seqName, start, end, opts) {
+        if (!this.index) {
+            return [];
+        }
+        await this.index.parse();
+        const seqId = this.chrToIndex?.[seqName];
+        return seqId === undefined
+            ? []
+            : this.index.blocksForRange(seqId, start, end, opts);
     }
 }
 exports.default = BamFile;