npm - @gmod/bam - Versions diffs - 4.0.0 → 5.0.0 - Mend

@gmod/bam 4.0.0 → 5.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (68) hide show

package/dist/record.js CHANGED Viewed

@@ -7,21 +7,25 @@ const constants_1 = __importDefault(require("./constants"));
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
 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;
@@ -53,10 +57,13 @@ 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 +
@@ -65,45 +72,45 @@ 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));
                     }
@@ -114,15 +121,15 @@ 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);
@@ -133,7 +140,7 @@ 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;
@@ -143,7 +150,7 @@ 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);
@@ -154,7 +161,7 @@ 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;
@@ -163,7 +170,7 @@ 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;
@@ -171,7 +178,7 @@ 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;
@@ -179,7 +186,7 @@ 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;
@@ -187,7 +194,7 @@ 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;
@@ -195,7 +202,7 @@ 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;
@@ -271,14 +278,14 @@ 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') {
@@ -292,7 +299,7 @@ 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);
@@ -375,25 +382,25 @@ 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/dist/record.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/util.d.ts CHANGED Viewed

@@ -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/dist/util.js CHANGED Viewed

@@ -1,13 +1,4 @@
 "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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -21,6 +12,8 @@ exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
 exports.findFirstData = findFirstData;
 exports.parseNameBytes = parseNameBytes;
+exports.sum = sum;
+exports.concatUint8Array = concatUint8Array;
 const long_1 = __importDefault(require("long"));
 function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
@@ -59,11 +52,9 @@ function checkAbortSignal(signal) {
  * provide a place to break when an abort signal is received.
  * @param {AbortSignal} signal
  */
-function abortBreakPoint(signal) {
-    return __awaiter(this, void 0, void 0, function* () {
-        yield Promise.resolve();
-        checkAbortSignal(signal);
-    });
+async function abortBreakPoint(signal) {
+    await Promise.resolve();
+    checkAbortSignal(signal);
 }
 function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
@@ -123,7 +114,10 @@ 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;
@@ -134,4 +128,20 @@ function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     }
     return { refNameToId, refIdToName };
 }
+function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+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/dist/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/virtualOffset.d.ts CHANGED Viewed

@@ -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/dist/virtualOffset.js CHANGED Viewed

@@ -2,6 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fromBytes = fromBytes;
 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/dist/virtualOffset.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAgCA,8BAcC;AA9CD,MAAqB,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;AA/BD,gCA+BC;AACD,SAAgB,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/esm/bai.d.ts CHANGED Viewed

@@ -5,7 +5,7 @@ import IndexFile from './indexFile';
 export default class BAI extends IndexFile {
     setupP?: ReturnType<BAI['_parse']>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
-    _parse(opts?: BaseOpts): Promise<{
+    _parse(_opts?: BaseOpts): Promise<{
         bai: boolean;
         firstDataLine: VirtualOffset | undefined;
         maxBlockSize: number;

package/esm/bai.js CHANGED Viewed

@@ -21,19 +21,20 @@ function reg2bins(beg, end) {
     ];
 }
 export default class BAI extends IndexFile {
+    setupP;
     async lineCount(refId, opts) {
-        var _a, _b;
         const indexData = await this.parse(opts);
-        return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
+        return indexData.indices[refId]?.stats?.lineCount || 0;
     }
     // fetch and parse the index
-    async _parse(opts) {
-        const bytes = (await this.filehandle.readFile(opts));
+    async _parse(_opts) {
+        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;
         // read the indexes for each reference sequence
@@ -42,12 +43,12 @@ export default class BAI extends IndexFile {
         const indices = new Array(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 = {};
             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;
@@ -58,7 +59,7 @@ export default class BAI extends IndexFile {
                     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(chunkCount);
                     for (let k = 0; k < chunkCount; k++) {
@@ -72,7 +73,7 @@ export default class BAI extends IndexFile {
                     binIndex[bin] = chunks;
                 }
             }
-            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
@@ -127,7 +128,7 @@ export default class BAI extends IndexFile {
         }
         return depths.map(d => ({
             ...d,
-            score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize,
+            score: (d.score * (stats?.lineCount || 0)) / totalSize,
         }));
     }
     async blocksForRange(refId, min, max, opts = {}) {
@@ -184,9 +185,8 @@ export default class BAI extends IndexFile {
         return this.setupP;
     }
     async hasRefSeq(seqId, opts = {}) {
-        var _a;
         const header = await this.parse(opts);
-        return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+        return !!header.indices[seqId]?.binIndex;
     }
 }
 //# sourceMappingURL=bai.js.map

package/esm/bai.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/esm/bamFile.d.ts CHANGED Viewed

@@ -1,5 +1,4 @@
-import { Buffer } from 'buffer';
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import BAI from './bai';
 import CSI from './csi';
 import Chunk from './chunk';
@@ -60,17 +59,17 @@ export default class BamFile {
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
-    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Buffer>;
+    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Uint8Array<ArrayBuffer>>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: Buffer;
+        data: Uint8Array<ArrayBuffer>;
         cpositions: number[];
         dpositions: number[];
         chunk: Chunk;
     }>;
-    readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
     hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{