@gmod/bam 6.1.0 → 7.0.0

package/esm/record.js

@@ -1,36 +1,31 @@
-var __classPrivateFieldSet = (this && this.__classPrivateFieldSet) || function (receiver, state, value, kind, f) {
-    if (kind === "m") throw new TypeError("Private method is not writable");
-    if (kind === "a" && !f) throw new TypeError("Private accessor was defined without a setter");
-    if (typeof state === "function" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError("Cannot write private member to an object whose class did not declare it");
-    return (kind === "a" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;
-};
-var __classPrivateFieldGet = (this && this.__classPrivateFieldGet) || function (receiver, state, kind, f) {
-    if (kind === "a" && !f) throw new TypeError("Private accessor was defined without a getter");
-    if (typeof state === "function" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError("Cannot read private member from an object whose class did not declare it");
-    return kind === "m" ? f : kind === "a" ? f.call(receiver) : f ? f.value : state.get(receiver);
-};
-var _BamRecord_dataView;
 import Constants from "./constants.js";
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
-const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
-class BamRecord {
+const ASCII_CIGAR_CODES = [
+    77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
+];
+// const CIGAR_MATCH = 0
+const CIGAR_INS = 1;
+// const CIGAR_DEL = 2
+const CIGAR_REF_SKIP = 3;
+const CIGAR_SOFT_CLIP = 4;
+const CIGAR_HARD_CLIP = 5;
+export default class BamRecord {
     constructor(args) {
-        _BamRecord_dataView.set(this, void 0);
         this.bytes = args.bytes;
         this.fileOffset = args.fileOffset;
-        __classPrivateFieldSet(this, _BamRecord_dataView, new DataView(this.bytes.byteArray.buffer), "f");
+        this._dataView = new DataView(this.bytes.byteArray.buffer);
     }
     get byteArray() {
         return this.bytes.byteArray;
     }
     get flags() {
-        return ((__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 16, true) & 0xffff0000) >> 16);
+        return ((this._dataView.getInt32(this.bytes.start + 16, true) & 0xffff0000) >> 16);
     }
     get ref_id() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 4, true);
+        return this._dataView.getInt32(this.bytes.start + 4, true);
     }
     get start() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 8, true);
+        return this._dataView.getInt32(this.bytes.start + 8, true);
     }
     get end() {
         return this.start + this.length_on_ref;
@@ -77,145 +72,103 @@ class BamRecord {
         const blockEnd = this.bytes.end;
         const tags = {};
         while (p < blockEnd) {
-            const tag = String.fromCharCode(this.byteArray[p], this.byteArray[p + 1]);
+            const tag = String.fromCharCode(this.byteArray[p]) +
+                String.fromCharCode(this.byteArray[p + 1]);
             const type = String.fromCharCode(this.byteArray[p + 2]);
             p += 3;
-            if (type === 'A') {
-                tags[tag] = String.fromCharCode(this.byteArray[p]);
-                p += 1;
-            }
-            else if (type === 'i') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-                p += 4;
-            }
-            else if (type === 'I') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true);
-                p += 4;
-            }
-            else if (type === 'c') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt8(p);
-                p += 1;
-            }
-            else if (type === 'C') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint8(p);
-                p += 1;
-            }
-            else if (type === 's') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt16(p, true);
-                p += 2;
-            }
-            else if (type === 'S') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint16(p, true);
-                p += 2;
-            }
-            else if (type === 'f') {
-                tags[tag] = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getFloat32(p, true);
-                p += 4;
-            }
-            else if (type === 'Z' || type === 'H') {
-                const value = [];
-                while (p <= blockEnd) {
-                    const cc = this.byteArray[p++];
-                    if (cc !== 0) {
-                        value.push(String.fromCharCode(cc));
-                    }
-                    else {
-                        break;
-                    }
-                }
-                tags[tag] = value.join('');
-            }
-            else if (type === 'B') {
-                const cc = this.byteArray[p++];
-                const Btype = String.fromCharCode(cc);
-                const limit = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-                p += 4;
-                if (Btype === 'i') {
-                    if (tag === 'CG') {
-                        const value = [];
-                        for (let k = 0; k < limit; k++) {
-                            const cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-                            const lop = cigop >> 4;
-                            const op = CIGAR_DECODER[cigop & 0xf];
-                            value.push(lop + op);
-                            p += 4;
+            switch (type) {
+                case 'A':
+                    tags[tag] = String.fromCharCode(this.byteArray[p]);
+                    p += 1;
+                    break;
+                case 'i':
+                    tags[tag] = this._dataView.getInt32(p, true);
+                    p += 4;
+                    break;
+                case 'I':
+                    tags[tag] = this._dataView.getUint32(p, true);
+                    p += 4;
+                    break;
+                case 'c':
+                    tags[tag] = this._dataView.getInt8(p);
+                    p += 1;
+                    break;
+                case 'C':
+                    tags[tag] = this._dataView.getUint8(p);
+                    p += 1;
+                    break;
+                case 's':
+                    tags[tag] = this._dataView.getInt16(p, true);
+                    p += 2;
+                    break;
+                case 'S':
+                    tags[tag] = this._dataView.getUint16(p, true);
+                    p += 2;
+                    break;
+                case 'f':
+                    tags[tag] = this._dataView.getFloat32(p, true);
+                    p += 4;
+                    break;
+                case 'Z':
+                case 'H': {
+                    const value = [];
+                    while (p <= blockEnd) {
+                        const cc = this.byteArray[p++];
+                        if (cc !== 0) {
+                            value.push(String.fromCharCode(cc));
                         }
-                        tags[tag] = value.join('');
-                    }
-                    else {
-                        const value = [];
-                        for (let k = 0; k < limit; k++) {
-                            value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true));
-                            p += 4;
+                        else {
+                            break;
                         }
-                        tags[tag] = value;
                     }
+                    tags[tag] = value.join('');
+                    break;
                 }
-                else if (Btype === 'I') {
-                    if (tag === 'CG') {
-                        const value = [];
-                        for (let k = 0; k < limit; k++) {
-                            const cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true);
-                            const lop = cigop >> 4;
-                            const op = CIGAR_DECODER[cigop & 0xf];
-                            value.push(lop + op);
-                            p += 4;
-                        }
-                        tags[tag] = value.join('');
+                case 'B': {
+                    const cc = this.byteArray[p++];
+                    const Btype = String.fromCharCode(cc);
+                    const limit = this._dataView.getInt32(p, true);
+                    p += 4;
+                    if (Btype === 'i') {
+                        const bytes = this.byteArray.slice(p, p + limit * 4);
+                        tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit * 4;
                     }
-                    else {
-                        const value = [];
-                        for (let k = 0; k < limit; k++) {
-                            value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint32(p, true));
-                            p += 4;
-                        }
-                        tags[tag] = value;
+                    else if (Btype === 'I') {
+                        const bytes = this.byteArray.slice(p, p + limit * 4);
+                        tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit * 4;
                     }
-                }
-                else if (Btype === 's') {
-                    const value = [];
-                    for (let k = 0; k < limit; k++) {
-                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt16(p, true));
-                        p += 2;
+                    else if (Btype === 's') {
+                        const bytes = this.byteArray.slice(p, p + limit * 2);
+                        tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit * 2;
                     }
-                    tags[tag] = value;
-                }
-                else if (Btype === 'S') {
-                    const value = [];
-                    for (let k = 0; k < limit; k++) {
-                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint16(p, true));
-                        p += 2;
+                    else if (Btype === 'S') {
+                        const bytes = this.byteArray.slice(p, p + limit * 2);
+                        tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit * 2;
                     }
-                    tags[tag] = value;
-                }
-                else if (Btype === 'c') {
-                    const value = [];
-                    for (let k = 0; k < limit; k++) {
-                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt8(p));
-                        p += 1;
+                    else if (Btype === 'c') {
+                        const bytes = this.byteArray.slice(p, p + limit);
+                        tags[tag] = new Int8Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit;
                     }
-                    tags[tag] = value;
-                }
-                else if (Btype === 'C') {
-                    const value = [];
-                    for (let k = 0; k < limit; k++) {
-                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getUint8(p));
-                        p += 1;
+                    else if (Btype === 'C') {
+                        const bytes = this.byteArray.slice(p, p + limit);
+                        tags[tag] = new Uint8Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit;
                     }
-                    tags[tag] = value;
-                }
-                else if (Btype === 'f') {
-                    const value = [];
-                    for (let k = 0; k < limit; k++) {
-                        value.push(__classPrivateFieldGet(this, _BamRecord_dataView, "f").getFloat32(p, true));
-                        p += 4;
+                    else if (Btype === 'f') {
+                        const bytes = this.byteArray.slice(p, p + limit * 4);
+                        tags[tag] = new Float32Array(bytes.buffer, bytes.byteOffset, limit);
+                        p += limit * 4;
                     }
-                    tags[tag] = value;
+                    break;
                 }
-            }
-            else {
-                console.error('Unknown BAM tag type', type);
-                break;
+                default:
+                    console.error('Unknown BAM tag type', type);
+                    break;
             }
         }
         return tags;
@@ -275,48 +228,49 @@ class BamRecord {
         if (this.isSegmentUnmapped()) {
             return {
                 length_on_ref: 0,
-                CIGAR: '',
+                NUMERIC_CIGAR: new Uint32Array(0),
             };
         }
         const numCigarOps = this.num_cigar_ops;
         let p = this.b0 + this.read_name_length;
-        const CIGAR = [];
         // check for CG tag by inspecting whether the CIGAR field contains a clip
         // that consumes entire seqLen
-        let cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-        let lop = cigop >> 4;
-        let op = CIGAR_DECODER[cigop & 0xf];
-        if (op === 'S' && lop === this.seq_length) {
+        const cigop = this._dataView.getInt32(p, true);
+        const lop = cigop >> 4;
+        const op = cigop & 0xf;
+        if (op === CIGAR_SOFT_CLIP && 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 = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-            lop = cigop >> 4;
-            op = CIGAR_DECODER[cigop & 0xf];
-            if (op !== 'N') {
+            const cigop = this._dataView.getInt32(p, true);
+            const lop = cigop >> 4;
+            const op = cigop & 0xf;
+            if (op !== CIGAR_REF_SKIP) {
                 console.warn('CG tag with no N tag');
             }
+            const cgArray = this.tags.CG;
             return {
-                CIGAR: this.tags.CG,
+                NUMERIC_CIGAR: cgArray,
                 length_on_ref: lop,
             };
         }
         else {
+            const cigarBytes = this.byteArray.slice(p, p + numCigarOps * 4);
+            const cigarView = new Uint32Array(cigarBytes.buffer, cigarBytes.byteOffset, numCigarOps);
             let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
-                cigop = __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(p, true);
-                lop = cigop >> 4;
-                op = CIGAR_DECODER[cigop & 0xf];
-                CIGAR.push(lop + op);
+                const cigop = cigarView[c];
+                const op = cigop & 0xf;
                 // soft clip, hard clip, and insertion don't count toward the length on
                 // the reference
-                if (op !== 'H' && op !== 'S' && op !== 'I') {
-                    lref += lop;
+                if (op !== CIGAR_HARD_CLIP &&
+                    op !== CIGAR_SOFT_CLIP &&
+                    op !== CIGAR_INS) {
+                    lref += cigop >> 4;
                 }
-                p += 4;
             }
             return {
-                CIGAR: CIGAR.join(''),
+                NUMERIC_CIGAR: cigarView,
                 length_on_ref: lref,
             };
         }
@@ -324,8 +278,19 @@ class BamRecord {
     get length_on_ref() {
         return this.cigarAndLength.length_on_ref;
     }
+    get NUMERIC_CIGAR() {
+        return this.cigarAndLength.NUMERIC_CIGAR;
+    }
     get CIGAR() {
-        return this.cigarAndLength.CIGAR;
+        const numeric = this.NUMERIC_CIGAR;
+        let result = '';
+        for (let i = 0, l = numeric.length; i < l; i++) {
+            const packed = numeric[i];
+            const length = packed >> 4;
+            const opCode = ASCII_CIGAR_CODES[packed & 0xf];
+            result += length + String.fromCharCode(opCode);
+        }
+        return result;
     }
     get num_cigar_ops() {
         return this.flag_nc & 0xffff;
@@ -338,18 +303,18 @@ class BamRecord {
     }
     get seq() {
         const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
-        const seqBytes = this.num_seq_bytes;
         const len = this.seq_length;
-        const buf = [];
+        const buf = new Array(len);
         let i = 0;
-        for (let j = 0; j < seqBytes; ++j) {
+        const fullBytes = len >> 1;
+        for (let j = 0; j < fullBytes; ++j) {
             const sb = this.byteArray[p + j];
-            buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
-            i++;
-            if (i < len) {
-                buf.push(SEQRET_DECODER[sb & 0x0f]);
-                i++;
-            }
+            buf[i++] = SEQRET_DECODER[(sb & 0xf0) >> 4];
+            buf[i++] = SEQRET_DECODER[sb & 0x0f];
+        }
+        if (i < len) {
+            const sb = this.byteArray[p + fullBytes];
+            buf[i] = SEQRET_DECODER[(sb & 0xf0) >> 4];
         }
         return buf.join('');
     }
@@ -389,22 +354,34 @@ class BamRecord {
         return undefined;
     }
     get bin_mq_nl() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 12, true);
+        return this._dataView.getInt32(this.bytes.start + 12, true);
     }
     get flag_nc() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 16, true);
+        return this._dataView.getInt32(this.bytes.start + 16, true);
     }
     get seq_length() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 20, true);
+        return this._dataView.getInt32(this.bytes.start + 20, true);
     }
     get next_refid() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 24, true);
+        return this._dataView.getInt32(this.bytes.start + 24, true);
     }
     get next_pos() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 28, true);
+        return this._dataView.getInt32(this.bytes.start + 28, true);
     }
     get template_length() {
-        return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 32, true);
+        return this._dataView.getInt32(this.bytes.start + 32, true);
+    }
+    seqAt(idx) {
+        if (idx < this.seq_length) {
+            const byteIndex = idx >> 1;
+            const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex];
+            return idx % 2 === 0
+                ? SEQRET_DECODER[(sb & 0xf0) >> 4]
+                : SEQRET_DECODER[sb & 0x0f];
+        }
+        else {
+            return undefined;
+        }
     }
     toJSON() {
         const data = {};
@@ -418,8 +395,6 @@ class BamRecord {
         return data;
     }
 }
-_BamRecord_dataView = new WeakMap();
-export default BamRecord;
 function cacheGetter(ctor, prop) {
     const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
     if (!desc) {
@@ -442,4 +417,5 @@ cacheGetter(BamRecord, 'tags');
 cacheGetter(BamRecord, 'cigarAndLength');
 cacheGetter(BamRecord, 'seq');
 cacheGetter(BamRecord, 'qual');
+cacheGetter(BamRecord, 'end');
 //# sourceMappingURL=record.js.map

package/esm/record.js.map

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

@@ -1,26 +1,5 @@
 import Chunk from './chunk.ts';
 import { Offset, VirtualOffset } from './virtualOffset.ts';
-export declare function timeout(ms: number): Promise<unknown>;
-/**
- * Properly check if the given AbortSignal is aborted.
- *
- * Per the standard, if the signal reads as aborted, this function throws
- * either a DOMException AbortError, or a regular error with a `code` attribute
- * set to `ERR_ABORTED`.
- *
- * For convenience, passing `undefined` is a no-op
- *
- * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
- * @returns nothing
- */
-export declare function checkAbortSignal(signal?: AbortSignal): void;
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- * @param {AbortSignal} signal
- */
-export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
 export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
 export interface BamOpts {
     viewAsPairs?: boolean;
@@ -41,6 +20,5 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
     refNameToId: Record<string, number>;
     refIdToName: string[];
 };
-export declare function sum(array: Uint8Array[]): number;
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
 export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;

package/esm/util.js

@@ -1,46 +1,4 @@
 import { longFromBytesToUnsigned } from "./long.js";
-export function timeout(ms) {
-    return new Promise(resolve => setTimeout(resolve, ms));
-}
-/**
- * Properly check if the given AbortSignal is aborted.
- *
- * Per the standard, if the signal reads as aborted, this function throws
- * either a DOMException AbortError, or a regular error with a `code` attribute
- * set to `ERR_ABORTED`.
- *
- * For convenience, passing `undefined` is a no-op
- *
- * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
- * @returns nothing
- */
-export function checkAbortSignal(signal) {
-    if (!signal) {
-        return;
-    }
-    if (signal.aborted) {
-        // console.log('bam aborted!')
-        if (typeof DOMException === 'undefined') {
-            const e = new Error('aborted');
-            // @ts-ignore
-            e.code = 'ERR_ABORTED';
-            throw e;
-        }
-        else {
-            throw new DOMException('aborted', 'AbortError');
-        }
-    }
-}
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- * @param {AbortSignal} signal
- */
-export async function abortBreakPoint(signal) {
-    await Promise.resolve();
-    checkAbortSignal(signal);
-}
 export function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
         chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
@@ -113,15 +71,12 @@ 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 totalLength = 0;
+    for (const entry of args) {
+        totalLength += entry.length;
+    }
+    const mergedArray = new Uint8Array(totalLength);
     let offset = 0;
     for (const entry of args) {
         mergedArray.set(entry, offset);
@@ -130,9 +85,11 @@ export function concatUint8Array(args) {
     return mergedArray;
 }
 export async function gen2array(gen) {
-    let out = [];
+    const out = [];
     for await (const x of gen) {
-        out = out.concat(x);
+        for (const item of x) {
+            out.push(item);
+        }
     }
     return out;
 }