npm - @gmod/bam - Versions diffs - 7.1.9 → 7.1.11 - Mend

@gmod/bam 7.1.9 → 7.1.11

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 (42) hide show

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 @@
1	- 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package/esm/util.d.ts CHANGED Viewed

@@ -1,11 +1,21 @@
 import Chunk from './chunk.ts';
 import { Offset, VirtualOffset } from './virtualOffset.ts';
 export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
+export interface TagFilter {
+    tag: string;
+    value?: string;
+}
+export interface FilterBy {
+    flagInclude?: number;
+    flagExclude?: number;
+    tagFilter?: TagFilter;
+}
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;
     maxInsertSize?: number;
     signal?: AbortSignal;
+    filterBy?: FilterBy;
 }
 export interface BaseOpts {
     signal?: AbortSignal;
@@ -22,3 +32,6 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 };
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
 export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;
+export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
+export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
+export declare function filterCacheKey(filterBy?: FilterBy): string;

package/esm/util.js CHANGED Viewed

@@ -122,4 +122,26 @@ export async function gen2array(gen) {
     }
     return out;
 }
+export function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    if (flags & flagExclude) {
+        return true;
+    }
+    return false;
+}
+export function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}
+export function filterCacheKey(filterBy) {
+    if (!filterBy) {
+        return '';
+    }
+    const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
+    const tagPart = tagFilter ? `:${tagFilter.tag}=${tagFilter.value ?? '*'}` : '';
+    return `:f${flagInclude}x${flagExclude}${tagPart}`;
+}
 //# sourceMappingURL=util.js.map

package/esm/util.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.9",
+  "version": "7.1.11",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",

package/src/bai.ts CHANGED Viewed

@@ -192,7 +192,7 @@ export default class BAI extends IndexFile {
     if (!seqIdx) {
       return []
     }
-    const { linearIndex = [], stats } = seqIdx
+    const { linearIndex, stats } = seqIdx
     if (linearIndex.length === 0) {
       return []
     }