@gmod/bam 4.0.0 → 5.0.0

package/esm/record.d.ts

@@ -1,17 +1,17 @@
-import type { Buffer } from 'buffer';
 interface Bytes {
     start: number;
     end: number;
-    byteArray: Buffer;
+    byteArray: Uint8Array;
 }
 export default class BamRecord {
+    #private;
     fileOffset: number;
     private bytes;
     constructor(args: {
         bytes: Bytes;
         fileOffset: number;
     });
-    get byteArray(): Buffer;
+    get byteArray(): Uint8Array<ArrayBufferLike>;
     get flags(): number;
     get ref_id(): number;
     get start(): number;
@@ -19,7 +19,7 @@ export default class BamRecord {
     get id(): number;
     get mq(): number | undefined;
     get score(): number | undefined;
-    get qual(): Buffer | undefined;
+    get qual(): Uint8Array<ArrayBufferLike> | undefined;
     get strand(): 1 | -1;
     get b0(): number;
     get name(): string;
@@ -61,7 +61,7 @@ export default class BamRecord {
     get read_name_length(): number;
     get num_seq_bytes(): number;
     get seq(): string;
-    get pair_orientation(): string;
+    get pair_orientation(): string | undefined;
     get bin_mq_nl(): number;
     get flag_nc(): number;
     get seq_length(): number;

package/esm/record.js

@@ -2,21 +2,25 @@ import Constants from './constants';
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
 export default class BamRecord {
+    fileOffset;
+    bytes;
+    #dataView;
     constructor(args) {
         this.bytes = args.bytes;
         this.fileOffset = args.fileOffset;
+        this.#dataView = new DataView(this.bytes.byteArray.buffer);
     }
     get byteArray() {
         return this.bytes.byteArray;
     }
     get flags() {
-        return ((this.byteArray.readInt32LE(this.bytes.start + 16) & 0xffff0000) >> 16);
+        return ((this.#dataView.getInt32(this.bytes.start + 16, true) & 0xffff0000) >> 16);
     }
     get ref_id() {
-        return this.byteArray.readInt32LE(this.bytes.start + 4);
+        return this.#dataView.getInt32(this.bytes.start + 4, true);
     }
     get start() {
-        return this.byteArray.readInt32LE(this.bytes.start + 8);
+        return this.#dataView.getInt32(this.bytes.start + 8, true);
     }
     get end() {
         return this.start + this.length_on_ref;
@@ -48,10 +52,13 @@ export default class BamRecord {
         return this.bytes.start + 36;
     }
     get name() {
-        return this.byteArray.toString('ascii', this.b0, this.b0 + this.read_name_length - 1);
+        let str = '';
+        for (let i = 0; i < this.read_name_length - 1; i++) {
+            str += String.fromCharCode(this.byteArray[this.b0 + i]);
+        }
+        return str;
     }
     get tags() {
-        const { byteArray } = this.bytes;
         let p = this.b0 +
             this.read_name_length +
             this.num_cigar_ops * 4 +
@@ -60,45 +67,45 @@ export default class BamRecord {
         const blockEnd = this.bytes.end;
         const tags = {};
         while (p < blockEnd) {
-            const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
-            const type = String.fromCharCode(byteArray[p + 2]);
+            const tag = String.fromCharCode(this.byteArray[p], this.byteArray[p + 1]);
+            const type = String.fromCharCode(this.byteArray[p + 2]);
             p += 3;
             if (type === 'A') {
-                tags[tag] = String.fromCharCode(byteArray[p]);
+                tags[tag] = String.fromCharCode(this.byteArray[p]);
                 p += 1;
             }
             else if (type === 'i') {
-                tags[tag] = byteArray.readInt32LE(p);
+                tags[tag] = this.#dataView.getInt32(p, true);
                 p += 4;
             }
             else if (type === 'I') {
-                tags[tag] = byteArray.readUInt32LE(p);
+                tags[tag] = this.#dataView.getUint32(p, true);
                 p += 4;
             }
             else if (type === 'c') {
-                tags[tag] = byteArray.readInt8(p);
+                tags[tag] = this.#dataView.getInt8(p);
                 p += 1;
             }
             else if (type === 'C') {
-                tags[tag] = byteArray.readUInt8(p);
+                tags[tag] = this.#dataView.getUint8(p);
                 p += 1;
             }
             else if (type === 's') {
-                tags[tag] = byteArray.readInt16LE(p);
+                tags[tag] = this.#dataView.getInt16(p, true);
                 p += 2;
             }
             else if (type === 'S') {
-                tags[tag] = byteArray.readUInt16LE(p);
+                tags[tag] = this.#dataView.getUint16(p, true);
                 p += 2;
             }
             else if (type === 'f') {
-                tags[tag] = byteArray.readFloatLE(p);
+                tags[tag] = this.#dataView.getFloat32(p, true);
                 p += 4;
             }
             else if (type === 'Z' || type === 'H') {
                 const value = [];
                 while (p <= blockEnd) {
-                    const cc = byteArray[p++];
+                    const cc = this.byteArray[p++];
                     if (cc !== 0) {
                         value.push(String.fromCharCode(cc));
                     }
@@ -109,15 +116,15 @@ export default class BamRecord {
                 tags[tag] = value.join('');
             }
             else if (type === 'B') {
-                const cc = byteArray[p++];
+                const cc = this.byteArray[p++];
                 const Btype = String.fromCharCode(cc);
-                const limit = byteArray.readInt32LE(p);
+                const limit = this.#dataView.getInt32(p, true);
                 p += 4;
                 if (Btype === 'i') {
                     if (tag === 'CG') {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            const cigop = byteArray.readInt32LE(p);
+                            const cigop = this.#dataView.getInt32(p, true);
                             const lop = cigop >> 4;
                             const op = CIGAR_DECODER[cigop & 0xf];
                             value.push(lop + op);
@@ -128,7 +135,7 @@ export default class BamRecord {
                     else {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            value.push(byteArray.readInt32LE(p));
+                            value.push(this.#dataView.getInt32(p, true));
                             p += 4;
                         }
                         tags[tag] = value;
@@ -138,7 +145,7 @@ export default class BamRecord {
                     if (tag === 'CG') {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            const cigop = byteArray.readUInt32LE(p);
+                            const cigop = this.#dataView.getUint32(p, true);
                             const lop = cigop >> 4;
                             const op = CIGAR_DECODER[cigop & 0xf];
                             value.push(lop + op);
@@ -149,7 +156,7 @@ export default class BamRecord {
                     else {
                         const value = [];
                         for (let k = 0; k < limit; k++) {
-                            value.push(byteArray.readUInt32LE(p));
+                            value.push(this.#dataView.getUint32(p, true));
                             p += 4;
                         }
                         tags[tag] = value;
@@ -158,7 +165,7 @@ export default class BamRecord {
                 else if (Btype === 's') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(byteArray.readInt16LE(p));
+                        value.push(this.#dataView.getInt16(p, true));
                         p += 2;
                     }
                     tags[tag] = value;
@@ -166,7 +173,7 @@ export default class BamRecord {
                 else if (Btype === 'S') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(byteArray.readUInt16LE(p));
+                        value.push(this.#dataView.getUint16(p, true));
                         p += 2;
                     }
                     tags[tag] = value;
@@ -174,7 +181,7 @@ export default class BamRecord {
                 else if (Btype === 'c') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(byteArray.readInt8(p));
+                        value.push(this.#dataView.getInt8(p));
                         p += 1;
                     }
                     tags[tag] = value;
@@ -182,7 +189,7 @@ export default class BamRecord {
                 else if (Btype === 'C') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(byteArray.readUInt8(p));
+                        value.push(this.#dataView.getUint8(p));
                         p += 1;
                     }
                     tags[tag] = value;
@@ -190,7 +197,7 @@ export default class BamRecord {
                 else if (Btype === 'f') {
                     const value = [];
                     for (let k = 0; k < limit; k++) {
-                        value.push(byteArray.readFloatLE(p));
+                        value.push(this.#dataView.getFloat32(p, true));
                         p += 4;
                     }
                     tags[tag] = value;
@@ -266,14 +273,14 @@ export default class BamRecord {
         const CIGAR = [];
         // check for CG tag by inspecting whether the CIGAR field contains a clip
         // that consumes entire seqLen
-        let cigop = this.byteArray.readInt32LE(p);
+        let cigop = this.#dataView.getInt32(p, true);
         let lop = cigop >> 4;
         let op = CIGAR_DECODER[cigop & 0xf];
         if (op === 'S' && lop === this.seq_length) {
             // if there is a CG the second CIGAR field will be a N tag the represents
             // the length on ref
             p += 4;
-            cigop = this.byteArray.readInt32LE(p);
+            cigop = this.#dataView.getInt32(p, true);
             lop = cigop >> 4;
             op = CIGAR_DECODER[cigop & 0xf];
             if (op !== 'N') {
@@ -287,7 +294,7 @@ export default class BamRecord {
         else {
             let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
-                cigop = this.byteArray.readInt32LE(p);
+                cigop = this.#dataView.getInt32(p, true);
                 lop = cigop >> 4;
                 op = CIGAR_DECODER[cigop & 0xf];
                 CIGAR.push(lop + op);
@@ -370,25 +377,25 @@ export default class BamRecord {
             }
             return tmp.join('');
         }
-        return '';
+        return undefined;
     }
     get bin_mq_nl() {
-        return this.byteArray.readInt32LE(this.bytes.start + 12);
+        return this.#dataView.getInt32(this.bytes.start + 12, true);
     }
     get flag_nc() {
-        return this.byteArray.readInt32LE(this.bytes.start + 16);
+        return this.#dataView.getInt32(this.bytes.start + 16, true);
     }
     get seq_length() {
-        return this.byteArray.readInt32LE(this.bytes.start + 20);
+        return this.#dataView.getInt32(this.bytes.start + 20, true);
     }
     get next_refid() {
-        return this.byteArray.readInt32LE(this.bytes.start + 24);
+        return this.#dataView.getInt32(this.bytes.start + 24, true);
     }
     get next_pos() {
-        return this.byteArray.readInt32LE(this.bytes.start + 28);
+        return this.#dataView.getInt32(this.bytes.start + 28, true);
     }
     get template_length() {
-        return this.byteArray.readInt32LE(this.bytes.start + 32);
+        return this.#dataView.getInt32(this.bytes.start + 32, true);
     }
     toJSON() {
         const data = {};

package/esm/record.js.map

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package/esm/util.d.ts

@@ -32,11 +32,13 @@ export interface BaseOpts {
 }
 export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
 export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
-export declare function parsePseudoBin(bytes: Buffer, offset: number): {
+export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
 export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
-export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
+export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (arg: string) => string): {
     refNameToId: Record<string, number>;
     refIdToName: string[];
 };
+export declare function sum(array: Uint8Array[]): number;
+export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/esm/util.js

@@ -98,7 +98,10 @@ export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     for (let i = 0; i < namesBytes.length; i += 1) {
         if (!namesBytes[i]) {
             if (currNameStart < i) {
-                let refName = namesBytes.toString('utf8', currNameStart, i);
+                let refName = '';
+                for (let j = currNameStart; j < i; j++) {
+                    refName += String.fromCharCode(namesBytes[j]);
+                }
                 refName = renameRefSeq(refName);
                 refIdToName[currRefId] = refName;
                 refNameToId[refName] = currRefId;
@@ -109,4 +112,20 @@ export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     }
     return { refNameToId, refIdToName };
 }
+export function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+export function concatUint8Array(args) {
+    const mergedArray = new Uint8Array(sum(args));
+    let offset = 0;
+    for (const entry of args) {
+        mergedArray.set(entry, offset);
+        offset += entry.length;
+    }
+    return mergedArray;
+}
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -1 +1 @@
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package/esm/virtualOffset.d.ts

@@ -6,4 +6,4 @@ export default class VirtualOffset {
     compareTo(b: VirtualOffset): number;
     static min(...args: VirtualOffset[]): VirtualOffset;
 }
-export declare function fromBytes(bytes: Buffer, offset?: number, bigendian?: boolean): VirtualOffset;
+export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;

package/esm/virtualOffset.js

@@ -1,4 +1,6 @@
 export default class VirtualOffset {
+    blockPosition;
+    dataPosition;
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data

package/esm/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,aAAa;IACzB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "4.0.0",
+  "version": "5.0.0",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -23,8 +23,8 @@
     "test": "vitest",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "clean": "rimraf dist esm",
-    "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:esm": "tsc --outDir esm",
+    "build:es5": "tsc --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "prebuild": "npm run clean && npm run lint",
     "preversion": "npm run lint && npm test run && npm run build",
@@ -39,10 +39,9 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/bgzf-filehandle": "^1.4.4",
-    "buffer": "^6.0.3",
+    "@gmod/bgzf-filehandle": "^2.0.1",
     "crc": "^4.3.2",
-    "generic-filehandle": "^3.0.0",
+    "generic-filehandle2": "^0.0.2",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
@@ -52,6 +51,7 @@
     "@typescript-eslint/eslint-plugin": "^8.1.0",
     "@typescript-eslint/parser": "^8.1.0",
     "@vitest/coverage-v8": "^2.0.5",
+    "buffer": "^6.0.3",
     "eslint": "^9.9.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",

package/src/bai.ts

@@ -34,15 +34,16 @@ export default class BAI extends IndexFile {
   }
 
   // fetch and parse the index
-  async _parse(opts?: BaseOpts) {
-    const bytes = (await this.filehandle.readFile(opts)) as Buffer
+  async _parse(_opts?: BaseOpts) {
+    const bytes = await this.filehandle.readFile()
+    const dataView = new DataView(bytes.buffer)
 
     // check BAI magic numbers
-    if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
+    if (dataView.getUint32(0, true) !== BAI_MAGIC) {
       throw new Error('Not a BAI file')
     }
 
-    const refCount = bytes.readInt32LE(4)
+    const refCount = dataView.getInt32(4, true)
     const depth = 5
     const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7
 
@@ -57,16 +58,18 @@ export default class BAI extends IndexFile {
       linearIndex: LinearIndex
       stats?: { lineCount: number }
     }>(refCount)
+
     for (let i = 0; i < refCount; i++) {
       // the binning index
-      const binCount = bytes.readInt32LE(curr)
+
+      const binCount = dataView.getInt32(curr, true)
       let stats
 
       curr += 4
       const binIndex: Record<number, Chunk[]> = {}
 
       for (let j = 0; j < binCount; j += 1) {
-        const bin = bytes.readUInt32LE(curr)
+        const bin = dataView.getUint32(curr, true)
         curr += 4
         if (bin === binLimit + 1) {
           curr += 4
@@ -75,7 +78,7 @@ export default class BAI extends IndexFile {
         } else if (bin > binLimit + 1) {
           throw new Error('bai index contains too many bins, please use CSI')
         } else {
-          const chunkCount = bytes.readInt32LE(curr)
+          const chunkCount = dataView.getInt32(curr, true)
           curr += 4
           const chunks = new Array<Chunk>(chunkCount)
           for (let k = 0; k < chunkCount; k++) {
@@ -90,7 +93,7 @@ export default class BAI extends IndexFile {
         }
       }
 
-      const linearCount = bytes.readInt32LE(curr)
+      const linearCount = dataView.getInt32(curr, true)
       curr += 4
       // as we're going through the linear index, figure out the smallest
       // virtual offset in the indexes, which tells us where the BAM header