npm - @gmod/bam - Versions diffs - 7.1.8 → 7.1.10 - Mend

@gmod/bam 7.1.8 → 7.1.10

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 (23) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,11 @@
+## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
+## [7.1.9](https://github.com/GMOD/bam-js/compare/v7.1.8...v7.1.9) (2025-12-13)
 ## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)

package/dist/bamFile.d.ts CHANGED Viewed

@@ -20,6 +20,11 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
     fileOffset: number;
 }) => T;
 export declare const BAM_MAGIC = 21840194;
+interface ChunkEntry<T> {
+    minBlock: number;
+    maxBlock: number;
+    features: T[];
+}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -32,16 +37,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
-    cache: QuickLRU<string, {
-        bytesRead: number;
-        buffer: Uint8Array;
-        nextIn: number;
-    }>;
-    chunkFeatureCache: QuickLRU<string, {
-        minBlock: number;
-        maxBlock: number;
-        features: T[];
-    }>;
+    chunkFeatureCache: QuickLRU<string, ChunkEntry<T>>;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
         bamFilehandle?: GenericFilehandle;
@@ -107,3 +103,4 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         end: number;
     }[], opts?: BaseOpts): Promise<number>;
 }
+export {};

package/dist/bamFile.js CHANGED Viewed

@@ -19,12 +19,11 @@ const blockLen = 1 << 16;
 class BamFile {
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
         this.htsget = false;
-        this.cache = new quick_lru_1.default({
-            maxSize: 1000,
-        });
         // Cache for parsed features by chunk
         // When a new chunk overlaps a cached chunk, we evict the cached one
-        this.chunkFeatureCache = new quick_lru_1.default({ maxSize: 100 });
+        this.chunkFeatureCache = new quick_lru_1.default({
+            maxSize: 100,
+        });
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
         if (bamFilehandle) {
@@ -287,7 +286,7 @@ class BamFile {
     }
     async _readChunk({ chunk, opts }) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
-        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, this.cache);
+        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -366,7 +365,11 @@ class BamFile {
             if (refId === undefined) {
                 throw new Error(`Unknown reference name: ${r.refName}`);
             }
-            return { refId, start: r.start, end: r.end };
+            return {
+                refId,
+                start: r.start,
+                end: r.end,
+            };
         });
         return this.index.estimatedBytesForRegions(regionsWithIds, opts);
     }

package/dist/bamFile.js.map CHANGED Viewed

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

@@ -1,14 +1,17 @@
 import BamFile from './bamFile.ts';
 import Chunk from './chunk.ts';
+import BamRecord from './record.ts';
+import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
-export default class HtsgetFile extends BamFile {
+export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
     private baseUrl;
     private trackId;
     constructor(args: {
         trackId: string;
         baseUrl: string;
+        recordClass?: BamRecordClass<T>;
     });
-    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record.ts").default[], void, unknown>;
+    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
     _readChunk({ chunk }: {
         chunk: Chunk;
         opts: BaseOpts;

package/dist/htsget.js CHANGED Viewed

@@ -68,7 +68,7 @@ async function concat(arr, opts) {
 }
 class HtsgetFile extends bamFile_ts_1.default {
     constructor(args) {
-        super({ htsget: true });
+        super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }

package/dist/htsget.js.map CHANGED Viewed

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

@@ -5,13 +5,16 @@ export interface Bytes {
 }
 interface CIGAR_AND_LENGTH {
     length_on_ref: number;
-    NUMERIC_CIGAR: Uint32Array;
+    NUMERIC_CIGAR: Uint32Array | number[];
 }
 export default class BamRecord {
     fileOffset: number;
     private bytes;
     private _dataView;
     private _cachedFlags?;
+    private _cachedRefId?;
+    private _cachedStart?;
+    private _cachedEnd?;
     private _cachedTags?;
     private _cachedCigarAndLength?;
     private _cachedNUMERIC_MD?;
@@ -48,7 +51,7 @@ export default class BamRecord {
     get cigarAndLength(): CIGAR_AND_LENGTH;
     private _computeCigarAndLength;
     get length_on_ref(): number;
-    get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
+    get NUMERIC_CIGAR(): number[] | Uint32Array<ArrayBufferLike>;
     get CIGAR(): string;
     get num_cigar_ops(): number;
     get num_cigar_bytes(): number;

package/dist/record.js CHANGED Viewed

@@ -29,13 +29,22 @@ class BamRecord {
         return this._cachedFlags;
     }
     get ref_id() {
-        return this._dataView.getInt32(this.bytes.start + 4, true);
+        if (this._cachedRefId === undefined) {
+            this._cachedRefId = this._dataView.getInt32(this.bytes.start + 4, true);
+        }
+        return this._cachedRefId;
     }
     get start() {
-        return this._dataView.getInt32(this.bytes.start + 8, true);
+        if (this._cachedStart === undefined) {
+            this._cachedStart = this._dataView.getInt32(this.bytes.start + 8, true);
+        }
+        return this._cachedStart;
     }
     get end() {
-        return this.start + this.length_on_ref;
+        if (this._cachedEnd === undefined) {
+            this._cachedEnd = this.start + this.length_on_ref;
+        }
+        return this._cachedEnd;
     }
     get mq() {
         const mq = (this.bin_mq_nl & 0xff00) >> 8;
@@ -62,12 +71,16 @@ class BamRecord {
     get b0() {
         return this.bytes.start + 36;
     }
+    // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
     get name() {
-        let str = '';
-        for (let i = 0; i < this.read_name_length - 1; i++) {
-            str += String.fromCharCode(this.byteArray[this.b0 + i]);
+        const len = this.read_name_length - 1;
+        const start = this.b0;
+        const ba = this.byteArray;
+        const codes = new Array(len);
+        for (let i = 0; i < len; i++) {
+            codes[i] = ba[start + i];
         }
-        return str;
+        return String.fromCharCode(...codes);
     }
     get NUMERIC_MD() {
         if (this._cachedNUMERIC_MD === undefined) {
@@ -323,6 +336,24 @@ class BamRecord {
         }
         return this._cachedCigarAndLength;
     }
+    // Benchmark results for CIGAR parsing strategies (see benchmarks/cigar-lifecycle.bench.ts):
+    //
+    // Aligned data:
+    //   - Plain array is 1.6-1.8x faster than Uint32Array for small CIGARs (≤50 ops)
+    //   - Uint32Array view is 1.3-2.2x faster for large CIGARs (≥200 ops)
+    //   - Crossover point is around 50-100 ops
+    //
+    // Unaligned data (requires slice+copy for Uint32Array):
+    //   - Plain array is 3.7-6.1x faster for typical sizes (50-200 ops)
+    //   - Plain array is 9-10x faster for small CIGARs (1-7 ops)
+    //   - Uint32Array slice+copy only wins at extreme sizes (10000 ops: 1.4x faster)
+    //
+    // Using |0 to force 32-bit integers in plain array path:
+    //   - 1.67x faster for medium CIGARs (50 ops)
+    //   - Neutral for small CIGARs (1-7 ops)
+    //
+    // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
+    // Uint32Array view only for large aligned CIGARs.
     _computeCigarAndLength() {
         if (this.isSegmentUnmapped()) {
             return {
@@ -354,19 +385,34 @@ class BamRecord {
             };
         }
         const absOffset = this.byteArray.byteOffset + p;
-        const cigarView = absOffset % 4 === 0
-            ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
-            : new Uint32Array(this.byteArray.slice(p, p + (numCigarOps << 2)).buffer, 0, numCigarOps);
+        const isAligned = absOffset % 4 === 0;
+        if (isAligned && numCigarOps > 50) {
+            const cigarView = new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps);
+            let lref = 0;
+            for (let c = 0; c < numCigarOps; ++c) {
+                const cigop = cigarView[c];
+                const op = cigop & 0xf;
+                if (!((1 << op) & CIGAR_SKIP_MASK)) {
+                    lref += cigop >> 4;
+                }
+            }
+            return {
+                NUMERIC_CIGAR: cigarView,
+                length_on_ref: lref,
+            };
+        }
+        const cigarArray = new Array(numCigarOps);
         let lref = 0;
         for (let c = 0; c < numCigarOps; ++c) {
-            const cigop = cigarView[c];
-            const op = cigop & 0xf;
+            const cigop = this._dataView.getInt32(p + c * 4, true) | 0;
+            cigarArray[c] = cigop;
+            const op = (cigop & 0xf) | 0;
             if (!((1 << op) & CIGAR_SKIP_MASK)) {
-                lref += cigop >> 4;
+                lref = (lref + (cigop >> 4)) | 0;
             }
         }
         return {
-            NUMERIC_CIGAR: cigarView,
+            NUMERIC_CIGAR: cigarArray,
             length_on_ref: lref,
         };
     }
@@ -421,6 +467,7 @@ class BamRecord {
         return buf.join('');
     }
     // adapted from igv.js
+    // uses template literal instead of array+join (6.4x faster, see benchmarks/string-building.bench.ts)
     get pair_orientation() {
         if (!this.isSegmentUnmapped() &&
             !this.isMateUnmapped() &&
@@ -437,21 +484,9 @@ class BamRecord {
                 o1 = '2';
                 o2 = '1';
             }
-            const tmp = [];
-            const isize = this.template_length;
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+            return this.template_length > 0
+                ? `${s1}${o1}${s2}${o2}`
+                : `${s2}${o2}${s1}${o1}`;
         }
         return undefined;
     }

package/dist/record.js.map CHANGED Viewed

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

@@ -20,6 +20,11 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
     fileOffset: number;
 }) => T;
 export declare const BAM_MAGIC = 21840194;
+interface ChunkEntry<T> {
+    minBlock: number;
+    maxBlock: number;
+    features: T[];
+}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -32,16 +37,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
-    cache: QuickLRU<string, {
-        bytesRead: number;
-        buffer: Uint8Array;
-        nextIn: number;
-    }>;
-    chunkFeatureCache: QuickLRU<string, {
-        minBlock: number;
-        maxBlock: number;
-        features: T[];
-    }>;
+    chunkFeatureCache: QuickLRU<string, ChunkEntry<T>>;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
         bamFilehandle?: GenericFilehandle;
@@ -107,3 +103,4 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         end: number;
     }[], opts?: BaseOpts): Promise<number>;
 }
+export {};

package/esm/bamFile.js CHANGED Viewed

@@ -13,12 +13,11 @@ const blockLen = 1 << 16;
 export default class BamFile {
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
         this.htsget = false;
-        this.cache = new QuickLRU({
-            maxSize: 1000,
-        });
         // Cache for parsed features by chunk
         // When a new chunk overlaps a cached chunk, we evict the cached one
-        this.chunkFeatureCache = new QuickLRU({ maxSize: 100 });
+        this.chunkFeatureCache = new QuickLRU({
+            maxSize: 100,
+        });
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? BAMFeature);
         if (bamFilehandle) {
@@ -281,7 +280,7 @@ export default class BamFile {
     }
     async _readChunk({ chunk, opts }) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
-        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
+        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -360,7 +359,11 @@ export default class BamFile {
             if (refId === undefined) {
                 throw new Error(`Unknown reference name: ${r.refName}`);
             }
-            return { refId, start: r.start, end: r.end };
+            return {
+                refId,
+                start: r.start,
+                end: r.end,
+            };
         });
         return this.index.estimatedBytesForRegions(regionsWithIds, opts);
     }

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -1,14 +1,17 @@
 import BamFile from './bamFile.ts';
 import Chunk from './chunk.ts';
+import BamRecord from './record.ts';
+import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
-export default class HtsgetFile extends BamFile {
+export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
     private baseUrl;
     private trackId;
     constructor(args: {
         trackId: string;
         baseUrl: string;
+        recordClass?: BamRecordClass<T>;
     });
-    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record.ts").default[], void, unknown>;
+    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
     _readChunk({ chunk }: {
         chunk: Chunk;
         opts: BaseOpts;

package/esm/htsget.js CHANGED Viewed

@@ -33,7 +33,7 @@ async function concat(arr, opts) {
 }
 export default class HtsgetFile extends BamFile {
     constructor(args) {
-        super({ htsget: true });
+        super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }

package/esm/htsget.js.map CHANGED Viewed

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

@@ -5,13 +5,16 @@ export interface Bytes {
 }
 interface CIGAR_AND_LENGTH {
     length_on_ref: number;
-    NUMERIC_CIGAR: Uint32Array;
+    NUMERIC_CIGAR: Uint32Array | number[];
 }
 export default class BamRecord {
     fileOffset: number;
     private bytes;
     private _dataView;
     private _cachedFlags?;
+    private _cachedRefId?;
+    private _cachedStart?;
+    private _cachedEnd?;
     private _cachedTags?;
     private _cachedCigarAndLength?;
     private _cachedNUMERIC_MD?;
@@ -48,7 +51,7 @@ export default class BamRecord {
     get cigarAndLength(): CIGAR_AND_LENGTH;
     private _computeCigarAndLength;
     get length_on_ref(): number;
-    get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
+    get NUMERIC_CIGAR(): number[] | Uint32Array<ArrayBufferLike>;
     get CIGAR(): string;
     get num_cigar_ops(): number;
     get num_cigar_bytes(): number;

package/esm/record.js CHANGED Viewed

@@ -24,13 +24,22 @@ export default class BamRecord {
         return this._cachedFlags;
     }
     get ref_id() {
-        return this._dataView.getInt32(this.bytes.start + 4, true);
+        if (this._cachedRefId === undefined) {
+            this._cachedRefId = this._dataView.getInt32(this.bytes.start + 4, true);
+        }
+        return this._cachedRefId;
     }
     get start() {
-        return this._dataView.getInt32(this.bytes.start + 8, true);
+        if (this._cachedStart === undefined) {
+            this._cachedStart = this._dataView.getInt32(this.bytes.start + 8, true);
+        }
+        return this._cachedStart;
     }
     get end() {
-        return this.start + this.length_on_ref;
+        if (this._cachedEnd === undefined) {
+            this._cachedEnd = this.start + this.length_on_ref;
+        }
+        return this._cachedEnd;
     }
     get mq() {
         const mq = (this.bin_mq_nl & 0xff00) >> 8;
@@ -57,12 +66,16 @@ export default class BamRecord {
     get b0() {
         return this.bytes.start + 36;
     }
+    // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
     get name() {
-        let str = '';
-        for (let i = 0; i < this.read_name_length - 1; i++) {
-            str += String.fromCharCode(this.byteArray[this.b0 + i]);
+        const len = this.read_name_length - 1;
+        const start = this.b0;
+        const ba = this.byteArray;
+        const codes = new Array(len);
+        for (let i = 0; i < len; i++) {
+            codes[i] = ba[start + i];
         }
-        return str;
+        return String.fromCharCode(...codes);
     }
     get NUMERIC_MD() {
         if (this._cachedNUMERIC_MD === undefined) {
@@ -318,6 +331,24 @@ export default class BamRecord {
         }
         return this._cachedCigarAndLength;
     }
+    // Benchmark results for CIGAR parsing strategies (see benchmarks/cigar-lifecycle.bench.ts):
+    //
+    // Aligned data:
+    //   - Plain array is 1.6-1.8x faster than Uint32Array for small CIGARs (≤50 ops)
+    //   - Uint32Array view is 1.3-2.2x faster for large CIGARs (≥200 ops)
+    //   - Crossover point is around 50-100 ops
+    //
+    // Unaligned data (requires slice+copy for Uint32Array):
+    //   - Plain array is 3.7-6.1x faster for typical sizes (50-200 ops)
+    //   - Plain array is 9-10x faster for small CIGARs (1-7 ops)
+    //   - Uint32Array slice+copy only wins at extreme sizes (10000 ops: 1.4x faster)
+    //
+    // Using |0 to force 32-bit integers in plain array path:
+    //   - 1.67x faster for medium CIGARs (50 ops)
+    //   - Neutral for small CIGARs (1-7 ops)
+    //
+    // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
+    // Uint32Array view only for large aligned CIGARs.
     _computeCigarAndLength() {
         if (this.isSegmentUnmapped()) {
             return {
@@ -349,19 +380,34 @@ export default class BamRecord {
             };
         }
         const absOffset = this.byteArray.byteOffset + p;
-        const cigarView = absOffset % 4 === 0
-            ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
-            : new Uint32Array(this.byteArray.slice(p, p + (numCigarOps << 2)).buffer, 0, numCigarOps);
+        const isAligned = absOffset % 4 === 0;
+        if (isAligned && numCigarOps > 50) {
+            const cigarView = new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps);
+            let lref = 0;
+            for (let c = 0; c < numCigarOps; ++c) {
+                const cigop = cigarView[c];
+                const op = cigop & 0xf;
+                if (!((1 << op) & CIGAR_SKIP_MASK)) {
+                    lref += cigop >> 4;
+                }
+            }
+            return {
+                NUMERIC_CIGAR: cigarView,
+                length_on_ref: lref,
+            };
+        }
+        const cigarArray = new Array(numCigarOps);
         let lref = 0;
         for (let c = 0; c < numCigarOps; ++c) {
-            const cigop = cigarView[c];
-            const op = cigop & 0xf;
+            const cigop = this._dataView.getInt32(p + c * 4, true) | 0;
+            cigarArray[c] = cigop;
+            const op = (cigop & 0xf) | 0;
             if (!((1 << op) & CIGAR_SKIP_MASK)) {
-                lref += cigop >> 4;
+                lref = (lref + (cigop >> 4)) | 0;
             }
         }
         return {
-            NUMERIC_CIGAR: cigarView,
+            NUMERIC_CIGAR: cigarArray,
             length_on_ref: lref,
         };
     }
@@ -416,6 +462,7 @@ export default class BamRecord {
         return buf.join('');
     }
     // adapted from igv.js
+    // uses template literal instead of array+join (6.4x faster, see benchmarks/string-building.bench.ts)
     get pair_orientation() {
         if (!this.isSegmentUnmapped() &&
             !this.isMateUnmapped() &&
@@ -432,21 +479,9 @@ export default class BamRecord {
                 o1 = '2';
                 o2 = '1';
             }
-            const tmp = [];
-            const isize = this.template_length;
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+            return this.template_length > 0
+                ? `${s1}${o1}${s2}${o2}`
+                : `${s2}${o2}${s1}${o1}`;
         }
         return undefined;
     }

package/esm/record.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.8",
+  "version": "7.1.10",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",

package/src/bamFile.ts CHANGED Viewed

@@ -34,6 +34,12 @@ export const BAM_MAGIC = 21840194
 const blockLen = 1 << 16
+interface ChunkEntry<T> {
+  minBlock: number
+  maxBlock: number
+  features: T[]
+}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
   public renameRefSeq: (a: string) => string
   public bam: GenericFilehandle
@@ -43,19 +49,12 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   public index?: BAI | CSI
   public htsget = false
   public headerP?: ReturnType<BamFile<T>['getHeaderPre']>
-  public cache = new QuickLRU<
-    string,
-    { bytesRead: number; buffer: Uint8Array; nextIn: number }
-  >({
-    maxSize: 1000,
-  })
   // Cache for parsed features by chunk
   // When a new chunk overlaps a cached chunk, we evict the cached one
-  public chunkFeatureCache = new QuickLRU<
-    string,
-    { minBlock: number; maxBlock: number; features: T[] }
-  >({ maxSize: 100 })
+  public chunkFeatureCache = new QuickLRU<string, ChunkEntry<T>>({
+    maxSize: 100,
+  })
   private RecordClass: BamRecordClass<T>
@@ -425,7 +424,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       buffer: data,
       cpositions,
       dpositions,
-    } = await unzipChunkSlice(buf, chunk, this.cache)
+    } = await unzipChunkSlice(buf, chunk)
     return { data, cpositions, dpositions, chunk }
   }
@@ -530,7 +529,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       if (refId === undefined) {
         throw new Error(`Unknown reference name: ${r.refName}`)
       }
-      return { refId, start: r.start, end: r.end }
+      return {
+        refId,
+        start: r.start,
+        end: r.end,
+      }
     })
     return this.index.estimatedBytesForRegions(regionsWithIds, opts)
   }

package/src/htsget.ts CHANGED Viewed

@@ -2,9 +2,11 @@ import { unzip } from '@gmod/bgzf-filehandle'
 import BamFile, { BAM_MAGIC } from './bamFile.ts'
 import Chunk from './chunk.ts'
+import BamRecord from './record.ts'
 import { parseHeaderText } from './sam.ts'
 import { concatUint8Array } from './util.ts'
+import type { BamRecordClass, BamRecordLike } from './bamFile.ts'
 import type { BamOpts, BaseOpts } from './util.ts'
 interface HtsgetChunk {
@@ -47,13 +49,19 @@ async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
   return concatUint8Array(await Promise.all(res.map(elt => unzip(elt))))
 }
-export default class HtsgetFile extends BamFile {
+export default class HtsgetFile<
+  T extends BamRecordLike = BamRecord,
+> extends BamFile<T> {
   private baseUrl: string
   private trackId: string
-  constructor(args: { trackId: string; baseUrl: string }) {
-    super({ htsget: true })
+  constructor(args: {
+    trackId: string
+    baseUrl: string
+    recordClass?: BamRecordClass<T>
+  }) {
+    super({ htsget: true, recordClass: args.recordClass })
     this.baseUrl = args.baseUrl
     this.trackId = args.trackId
   }

package/src/record.ts CHANGED Viewed

@@ -23,7 +23,7 @@ export interface Bytes {
 interface CIGAR_AND_LENGTH {
   length_on_ref: number
-  NUMERIC_CIGAR: Uint32Array
+  NUMERIC_CIGAR: Uint32Array | number[]
 }
 export default class BamRecord {
@@ -32,6 +32,9 @@ export default class BamRecord {
   private _dataView: DataView
   private _cachedFlags?: number
+  private _cachedRefId?: number
+  private _cachedStart?: number
+  private _cachedEnd?: number
   private _cachedTags?: Record<string, unknown>
   private _cachedCigarAndLength?: CIGAR_AND_LENGTH
   private _cachedNUMERIC_MD?: Uint8Array | null
@@ -55,15 +58,24 @@ export default class BamRecord {
     return this._cachedFlags
   }
   get ref_id() {
-    return this._dataView.getInt32(this.bytes.start + 4, true)
+    if (this._cachedRefId === undefined) {
+      this._cachedRefId = this._dataView.getInt32(this.bytes.start + 4, true)
+    }
+    return this._cachedRefId
   }
   get start() {
-    return this._dataView.getInt32(this.bytes.start + 8, true)
+    if (this._cachedStart === undefined) {
+      this._cachedStart = this._dataView.getInt32(this.bytes.start + 8, true)
+    }
+    return this._cachedStart
   }
   get end() {
-    return this.start + this.length_on_ref
+    if (this._cachedEnd === undefined) {
+      this._cachedEnd = this.start + this.length_on_ref
+    }
+    return this._cachedEnd
   }
   get mq() {
@@ -95,12 +107,16 @@ export default class BamRecord {
   get b0() {
     return this.bytes.start + 36
   }
+  // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
   get name() {
-    let str = ''
-    for (let i = 0; i < this.read_name_length - 1; i++) {
-      str += String.fromCharCode(this.byteArray[this.b0 + i]!)
+    const len = this.read_name_length - 1
+    const start = this.b0
+    const ba = this.byteArray
+    const codes = new Array(len)
+    for (let i = 0; i < len; i++) {
+      codes[i] = ba[start + i]!
     }
-    return str
+    return String.fromCharCode(...codes)
   }
   get NUMERIC_MD() {
@@ -370,6 +386,24 @@ export default class BamRecord {
     return this._cachedCigarAndLength
   }
+  // Benchmark results for CIGAR parsing strategies (see benchmarks/cigar-lifecycle.bench.ts):
+  //
+  // Aligned data:
+  //   - Plain array is 1.6-1.8x faster than Uint32Array for small CIGARs (≤50 ops)
+  //   - Uint32Array view is 1.3-2.2x faster for large CIGARs (≥200 ops)
+  //   - Crossover point is around 50-100 ops
+  //
+  // Unaligned data (requires slice+copy for Uint32Array):
+  //   - Plain array is 3.7-6.1x faster for typical sizes (50-200 ops)
+  //   - Plain array is 9-10x faster for small CIGARs (1-7 ops)
+  //   - Uint32Array slice+copy only wins at extreme sizes (10000 ops: 1.4x faster)
+  //
+  // Using |0 to force 32-bit integers in plain array path:
+  //   - 1.67x faster for medium CIGARs (50 ops)
+  //   - Neutral for small CIGARs (1-7 ops)
+  //
+  // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
+  // Uint32Array view only for large aligned CIGARs.
   private _computeCigarAndLength() {
     if (this.isSegmentUnmapped()) {
       return {
@@ -402,26 +436,42 @@ export default class BamRecord {
         length_on_ref: lop,
       }
     }
     const absOffset = this.byteArray.byteOffset + p
-    const cigarView =
-      absOffset % 4 === 0
-        ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
-        : new Uint32Array(
-            this.byteArray.slice(p, p + (numCigarOps << 2)).buffer,
-            0,
-            numCigarOps,
-          )
+    const isAligned = absOffset % 4 === 0
+    if (isAligned && numCigarOps > 50) {
+      const cigarView = new Uint32Array(
+        this.byteArray.buffer,
+        absOffset,
+        numCigarOps,
+      )
+      let lref = 0
+      for (let c = 0; c < numCigarOps; ++c) {
+        const cigop = cigarView[c]!
+        const op = cigop & 0xf
+        if (!((1 << op) & CIGAR_SKIP_MASK)) {
+          lref += cigop >> 4
+        }
+      }
+      return {
+        NUMERIC_CIGAR: cigarView,
+        length_on_ref: lref,
+      }
+    }
+    const cigarArray: number[] = new Array(numCigarOps)
     let lref = 0
     for (let c = 0; c < numCigarOps; ++c) {
-      const cigop = cigarView[c]!
-      const op = cigop & 0xf
+      const cigop = this._dataView.getInt32(p + c * 4, true) | 0
+      cigarArray[c] = cigop
+      const op = (cigop & 0xf) | 0
       if (!((1 << op) & CIGAR_SKIP_MASK)) {
-        lref += cigop >> 4
+        lref = (lref + (cigop >> 4)) | 0
       }
     }
     return {
-      NUMERIC_CIGAR: cigarView,
+      NUMERIC_CIGAR: cigarArray,
       length_on_ref: lref,
     }
   }
@@ -489,6 +539,7 @@ export default class BamRecord {
   }
   // adapted from igv.js
+  // uses template literal instead of array+join (6.4x faster, see benchmarks/string-building.bench.ts)
   get pair_orientation() {
     if (
       !this.isSegmentUnmapped() &&
@@ -507,20 +558,9 @@ export default class BamRecord {
         o2 = '1'
       }
-      const tmp = []
-      const isize = this.template_length
-      if (isize > 0) {
-        tmp[0] = s1
-        tmp[1] = o1
-        tmp[2] = s2
-        tmp[3] = o2
-      } else {
-        tmp[2] = s1
-        tmp[3] = o1
-        tmp[0] = s2
-        tmp[1] = o2
-      }
-      return tmp.join('')
+      return this.template_length > 0
+        ? `${s1}${o1}${s2}${o2}`
+        : `${s2}${o2}${s1}${o1}`
     }
     return undefined
   }