@gmod/bam 7.1.11 → 7.1.13

package/CHANGELOG.md

@@ -1,6 +1,10 @@
-## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
+## [7.1.13](https://github.com/GMOD/bam-js/compare/v7.1.12...v7.1.13) (2025-12-17)
+
 
 
+## [7.1.12](https://github.com/GMOD/bam-js/compare/v7.1.11...v7.1.12) (2025-12-17)
+
+## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
 
 ## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
 

package/README.md

@@ -140,6 +140,8 @@ record.template_length // TLEN
 
 // Auxiliary data
 record.tags // object with all aux tags e.g. {MD: "100", NM: 0}
+record.getTag('MD') // get a single tag (more efficient than record.tags when you only need one)
+record.getTagRaw('MD') // get tag as Uint8Array for string tags (avoids string conversion)
 record.NUMERIC_MD // MD tag as Uint8Array (for fast mismatch rendering)
 record.NUMERIC_CIGAR // Uint32Array of packed CIGAR operations
 record.NUMERIC_SEQ // Uint8Array of packed sequence (4-bit encoded)

package/dist/record.d.ts

@@ -18,6 +18,7 @@ export default class BamRecord {
     private _cachedTags?;
     private _cachedCigarAndLength?;
     private _cachedNUMERIC_MD?;
+    private _cachedTagsStart?;
     constructor(args: {
         bytes: Bytes;
         fileOffset: number;
@@ -32,9 +33,13 @@ export default class BamRecord {
     get qual(): Uint8Array<ArrayBufferLike> | null;
     get strand(): 1 | -1;
     get b0(): number;
+    get tagsStart(): number;
     get name(): string;
     get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
     get tags(): Record<string, unknown>;
+    getTag(tagName: string): unknown;
+    getTagRaw(tagName: string): string | number | number[] | Int8Array<ArrayBufferLike> | Uint8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
+    private _findTag;
     private _computeTags;
     isPaired(): boolean;
     isProperlyPaired(): boolean;

package/dist/record.js

@@ -9,8 +9,9 @@ const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const ASCII_CIGAR_CODES = [
     77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
 ];
-// ops that don't consume reference: INS, SOFT_CLIP, HARD_CLIP
-const CIGAR_SKIP_MASK = (1 << cigar_ts_1.CIGAR_INS) | (1 << cigar_ts_1.CIGAR_SOFT_CLIP) | (1 << cigar_ts_1.CIGAR_HARD_CLIP);
+// Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
+// Binary: 0b111001101 = 0x1CD
+const CIGAR_CONSUMES_REF_MASK = 0x1cd;
 class BamRecord {
     constructor(args) {
         this.bytes = args.bytes;
@@ -71,6 +72,17 @@ class BamRecord {
     get b0() {
         return this.bytes.start + 36;
     }
+    get tagsStart() {
+        if (this._cachedTagsStart === undefined) {
+            this._cachedTagsStart =
+                this.b0 +
+                    this.read_name_length +
+                    this.num_cigar_bytes +
+                    this.num_seq_bytes +
+                    this.seq_length;
+        }
+        return this._cachedTagsStart;
+    }
     // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
     get name() {
         const len = this.read_name_length - 1;
@@ -84,80 +96,195 @@ class BamRecord {
     }
     get NUMERIC_MD() {
         if (this._cachedNUMERIC_MD === undefined) {
-            let p = this.b0 +
-                this.read_name_length +
-                this.num_cigar_bytes +
-                this.num_seq_bytes +
-                this.seq_length;
-            const blockEnd = this.bytes.end;
-            const ba = this.byteArray;
-            while (p < blockEnd) {
-                const tag1 = ba[p];
-                const tag2 = ba[p + 1];
-                const type = ba[p + 2];
-                p += 3;
-                // 'M' = 0x4D, 'D' = 0x44, 'Z' = 0x5A
-                if (tag1 === 0x4d && tag2 === 0x44 && type === 0x5a) {
-                    const start = p;
-                    while (p < blockEnd && ba[p] !== 0) {
-                        p++;
+            const result = this.getTagRaw('MD');
+            this._cachedNUMERIC_MD = result instanceof Uint8Array ? result : null;
+        }
+        return this._cachedNUMERIC_MD === null ? undefined : this._cachedNUMERIC_MD;
+    }
+    get tags() {
+        if (this._cachedTags === undefined) {
+            this._cachedTags = this._computeTags();
+        }
+        return this._cachedTags;
+    }
+    getTag(tagName) {
+        if (this._cachedTags !== undefined) {
+            return this._cachedTags[tagName];
+        }
+        return this._findTag(tagName, false);
+    }
+    getTagRaw(tagName) {
+        return this._findTag(tagName, true);
+    }
+    _findTag(tagName, raw) {
+        const tag1 = tagName.charCodeAt(0);
+        const tag2 = tagName.charCodeAt(1);
+        let p = this.tagsStart;
+        const blockEnd = this.bytes.end;
+        const ba = this.byteArray;
+        while (p < blockEnd) {
+            const currentTag1 = ba[p];
+            const currentTag2 = ba[p + 1];
+            const type = ba[p + 2];
+            p += 3;
+            const isMatch = currentTag1 === tag1 && currentTag2 === tag2;
+            switch (type) {
+                case 0x41: // 'A'
+                    if (isMatch) {
+                        return String.fromCharCode(ba[p]);
+                    }
+                    p += 1;
+                    break;
+                case 0x69: // 'i'
+                    if (isMatch) {
+                        return this._dataView.getInt32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x49: // 'I'
+                    if (isMatch) {
+                        return this._dataView.getUint32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x63: // 'c'
+                    if (isMatch) {
+                        return this._dataView.getInt8(p);
+                    }
+                    p += 1;
+                    break;
+                case 0x43: // 'C'
+                    if (isMatch) {
+                        return this._dataView.getUint8(p);
+                    }
+                    p += 1;
+                    break;
+                case 0x73: // 's'
+                    if (isMatch) {
+                        return this._dataView.getInt16(p, true);
+                    }
+                    p += 2;
+                    break;
+                case 0x53: // 'S'
+                    if (isMatch) {
+                        return this._dataView.getUint16(p, true);
+                    }
+                    p += 2;
+                    break;
+                case 0x66: // 'f'
+                    if (isMatch) {
+                        return this._dataView.getFloat32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x5a: // 'Z'
+                case 0x48: {
+                    // 'H'
+                    if (isMatch) {
+                        const start = p;
+                        while (p < blockEnd && ba[p] !== 0) {
+                            p++;
+                        }
+                        if (raw) {
+                            return ba.subarray(start, p);
+                        }
+                        const value = [];
+                        for (let i = start; i < p; i++) {
+                            value.push(String.fromCharCode(ba[i]));
+                        }
+                        return value.join('');
                     }
-                    this._cachedNUMERIC_MD = ba.subarray(start, p);
+                    while (p <= blockEnd && ba[p++] !== 0) { }
+                    break;
                 }
-                switch (type) {
-                    case 0x41: // 'A'
-                        p += 1;
-                        break;
-                    case 0x69: // 'i'
-                    case 0x49: // 'I'
-                    case 0x66: // 'f'
-                        p += 4;
-                        break;
-                    case 0x63: // 'c'
-                    case 0x43: // 'C'
-                        p += 1;
-                        break;
-                    case 0x73: // 's'
-                    case 0x53: // 'S'
-                        p += 2;
-                        break;
-                    case 0x5a: // 'Z'
-                    case 0x48: // 'H'
-                        while (p <= blockEnd && ba[p++] !== 0) { }
-                        break;
-                    case 0x42: {
-                        // 'B'
-                        const Btype = ba[p++];
-                        const limit = this._dataView.getInt32(p, true);
-                        p += 4;
-                        if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
-                            p += limit << 2;
+                case 0x42: {
+                    // 'B'
+                    const Btype = ba[p++];
+                    const limit = this._dataView.getInt32(p, true);
+                    p += 4;
+                    const absOffset = ba.byteOffset + p;
+                    if (isMatch) {
+                        if (Btype === 0x69) {
+                            // 'i'
+                            if (absOffset % 4 === 0) {
+                                return new Int32Array(ba.buffer, absOffset, limit);
+                            }
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getInt32(p + i * 4, true);
+                            }
+                            return arr;
+                        }
+                        else if (Btype === 0x49) {
+                            // 'I'
+                            if (absOffset % 4 === 0) {
+                                return new Uint32Array(ba.buffer, absOffset, limit);
+                            }
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getUint32(p + i * 4, true);
+                            }
+                            return arr;
+                        }
+                        else if (Btype === 0x73) {
+                            // 's'
+                            if (absOffset % 2 === 0) {
+                                return new Int16Array(ba.buffer, absOffset, limit);
+                            }
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getInt16(p + i * 2, true);
+                            }
+                            return arr;
                         }
-                        else if (Btype === 0x73 || Btype === 0x53) {
-                            p += limit << 1;
+                        else if (Btype === 0x53) {
+                            // 'S'
+                            if (absOffset % 2 === 0) {
+                                return new Uint16Array(ba.buffer, absOffset, limit);
+                            }
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getUint16(p + i * 2, true);
+                            }
+                            return arr;
                         }
-                        else if (Btype === 0x63 || Btype === 0x43) {
-                            p += limit;
+                        else if (Btype === 0x63) {
+                            // 'c'
+                            return new Int8Array(ba.buffer, absOffset, limit);
                         }
-                        break;
+                        else if (Btype === 0x43) {
+                            // 'C'
+                            return new Uint8Array(ba.buffer, absOffset, limit);
+                        }
+                        else if (Btype === 0x66) {
+                            // 'f'
+                            if (absOffset % 4 === 0) {
+                                return new Float32Array(ba.buffer, absOffset, limit);
+                            }
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getFloat32(p + i * 4, true);
+                            }
+                            return arr;
+                        }
+                    }
+                    if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
+                        p += limit << 2;
+                    }
+                    else if (Btype === 0x73 || Btype === 0x53) {
+                        p += limit << 1;
+                    }
+                    else if (Btype === 0x63 || Btype === 0x43) {
+                        p += limit;
                     }
+                    break;
                 }
             }
         }
-        return this._cachedNUMERIC_MD === null ? undefined : this._cachedNUMERIC_MD;
-    }
-    get tags() {
-        if (this._cachedTags === undefined) {
-            this._cachedTags = this._computeTags();
-        }
-        return this._cachedTags;
+        return undefined;
     }
     _computeTags() {
-        let p = this.b0 +
-            this.read_name_length +
-            this.num_cigar_bytes +
-            this.num_seq_bytes +
-            this.seq_length;
+        let p = this.tagsStart;
         const blockEnd = this.bytes.end;
         const ba = this.byteArray;
         const tags = {};
@@ -226,8 +353,11 @@ class BamRecord {
                             tags[tag] = new Int32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit);
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getInt32(p + i * 4, true);
+                            }
+                            tags[tag] = arr;
                         }
                         p += limit << 2;
                     }
@@ -237,8 +367,11 @@ class BamRecord {
                             tags[tag] = new Uint32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit);
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getUint32(p + i * 4, true);
+                            }
+                            tags[tag] = arr;
                         }
                         p += limit << 2;
                     }
@@ -248,8 +381,11 @@ class BamRecord {
                             tags[tag] = new Int16Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 1));
-                            tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit);
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getInt16(p + i * 2, true);
+                            }
+                            tags[tag] = arr;
                         }
                         p += limit << 1;
                     }
@@ -259,8 +395,11 @@ class BamRecord {
                             tags[tag] = new Uint16Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 1));
-                            tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit);
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getUint16(p + i * 2, true);
+                            }
+                            tags[tag] = arr;
                         }
                         p += limit << 1;
                     }
@@ -280,8 +419,11 @@ class BamRecord {
                             tags[tag] = new Float32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Float32Array(bytes.buffer, bytes.byteOffset, limit);
+                            const arr = new Array(limit);
+                            for (let i = 0; i < limit; i++) {
+                                arr[i] = this._dataView.getFloat32(p + i * 4, true);
+                            }
+                            tags[tag] = arr;
                         }
                         p += limit << 2;
                     }
@@ -391,10 +533,7 @@ class BamRecord {
             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;
-                }
+                lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
             }
             return {
                 NUMERIC_CIGAR: cigarView,
@@ -406,10 +545,7 @@ class BamRecord {
         for (let c = 0; c < numCigarOps; ++c) {
             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 = (lref + (cigop >> 4)) | 0;
-            }
+            lref += (cigop >> 4) * ((CIGAR_CONSUMES_REF_MASK >> (cigop & 0xf)) & 1);
         }
         return {
             NUMERIC_CIGAR: cigarArray,

package/dist/record.js.map

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

@@ -18,6 +18,7 @@ export default class BamRecord {
     private _cachedTags?;
     private _cachedCigarAndLength?;
     private _cachedNUMERIC_MD?;
+    private _cachedTagsStart?;
     constructor(args: {
         bytes: Bytes;
         fileOffset: number;
@@ -32,9 +33,13 @@ export default class BamRecord {
     get qual(): Uint8Array<ArrayBufferLike> | null;
     get strand(): 1 | -1;
     get b0(): number;
+    get tagsStart(): number;
     get name(): string;
     get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
     get tags(): Record<string, unknown>;
+    getTag(tagName: string): unknown;
+    getTagRaw(tagName: string): string | number | number[] | Int8Array<ArrayBufferLike> | Uint8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
+    private _findTag;
     private _computeTags;
     isPaired(): boolean;
     isProperlyPaired(): boolean;