@gmod/bam 7.2.4 → 7.3.1

package/esm/record.js

@@ -18,6 +18,88 @@ const textDecoder = new TextDecoder();
 // 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;
+// Decode a 'B' (array) tag value starting at `p` (the byte after type+subtype+
+// count). When the data is naturally aligned we return a typed-array view over
+// the underlying buffer (zero-copy); otherwise we copy element-by-element since
+// typed-array views require alignment. Shared by getTag and the full-tag parse.
+function decodeBArrayTag(ba, dataView, p, Btype, limit) {
+    const absOffset = ba.byteOffset + p;
+    switch (Btype) {
+        case 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] = dataView.getInt32(p + i * 4, true);
+            }
+            return arr;
+        }
+        case 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] = dataView.getUint32(p + i * 4, true);
+            }
+            return arr;
+        }
+        case 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] = dataView.getInt16(p + i * 2, true);
+            }
+            return arr;
+        }
+        case 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] = dataView.getUint16(p + i * 2, true);
+            }
+            return arr;
+        }
+        case 0x63: // 'c'
+            return new Int8Array(ba.buffer, absOffset, limit);
+        case 0x43: // 'C'
+            return new Uint8Array(ba.buffer, absOffset, limit);
+        case 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] = dataView.getFloat32(p + i * 4, true);
+            }
+            return arr;
+        }
+        default:
+            return undefined;
+    }
+}
+// Byte span of a 'B' tag's element payload, for advancing the cursor past it.
+function bArrayByteLength(Btype, limit) {
+    if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
+        return limit << 2;
+    }
+    else if (Btype === 0x73 || Btype === 0x53) {
+        return limit << 1;
+    }
+    else {
+        return limit;
+    }
+}
 export default class BamRecord {
     fileOffset;
     _byteArray;
@@ -41,7 +123,10 @@ export default class BamRecord {
         return this._byteArray;
     }
     get flags() {
-        return (this._dataView.getInt32(this._start + 16, true) & 0xffff0000) >> 16;
+        // FLAG is the high 16 bits of flag_nc (byte offset 18). Read it directly as
+        // a uint16 — masking flag_nc and arithmetic-shifting would sign-extend any
+        // value >= 0x8000.
+        return this._dataView.getUint16(this._start + 18, true);
     }
     get ref_id() {
         return this._dataView.getInt32(this._start + 4, true);
@@ -62,12 +147,15 @@ export default class BamRecord {
     get score() {
         return this.mq;
     }
+    // QUAL is present whenever the record has bases — independent of the unmapped
+    // flag (unmapped reads routinely carry SEQ/QUAL). A zero-length SEQ means
+    // there is no quality to return.
     get qual() {
-        if (this.isSegmentUnmapped()) {
+        const seqLen = this.seq_length;
+        if (seqLen === 0) {
             return null;
         }
         else {
-            const seqLen = this.seq_length;
             const p = this.seqStart + ((seqLen + 1) >> 1);
             return this._byteArray.subarray(p, p + seqLen);
         }
@@ -205,83 +293,17 @@ export default class BamRecord {
                     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 === 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) {
-                            // 'c'
-                            return new Int8Array(ba.buffer, absOffset, limit);
-                        }
-                        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;
+                        return decodeBArrayTag(ba, this._dataView, p, Btype, limit);
                     }
+                    p += bArrayByteLength(Btype, limit);
                     break;
                 }
+                default:
+                    if (type !== undefined) {
+                        console.error('Unknown BAM tag type', type);
+                    }
+                    break;
             }
         }
         return undefined;
@@ -344,87 +366,8 @@ export default class BamRecord {
                     const Btype = ba[p++];
                     const limit = this._dataView.getInt32(p, true);
                     p += 4;
-                    const absOffset = ba.byteOffset + p;
-                    if (Btype === 0x69) {
-                        // 'i'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Int32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            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;
-                    }
-                    else if (Btype === 0x49) {
-                        // 'I'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Uint32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            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;
-                    }
-                    else if (Btype === 0x73) {
-                        // 's'
-                        if (absOffset % 2 === 0) {
-                            tags[tag] = new Int16Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            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;
-                    }
-                    else if (Btype === 0x53) {
-                        // 'S'
-                        if (absOffset % 2 === 0) {
-                            tags[tag] = new Uint16Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            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;
-                    }
-                    else if (Btype === 0x63) {
-                        // 'c'
-                        tags[tag] = new Int8Array(ba.buffer, absOffset, limit);
-                        p += limit;
-                    }
-                    else if (Btype === 0x43) {
-                        // 'C'
-                        tags[tag] = new Uint8Array(ba.buffer, absOffset, limit);
-                        p += limit;
-                    }
-                    else if (Btype === 0x66) {
-                        // 'f'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Float32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            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;
-                    }
+                    tags[tag] = decodeBArrayTag(ba, this._dataView, p, Btype, limit);
+                    p += bArrayByteLength(Btype, limit);
                     break;
                 }
                 default:
@@ -489,9 +432,15 @@ export default class BamRecord {
     // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
     // Uint32Array view only for large aligned CIGARs.
     // CG tag pattern: first op is soft-clip consuming entire sequence, second op is N encoding length-on-ref
-    _isCGTagPattern(p) {
-        const cigop = this._dataView.getInt32(p, true);
-        return (cigop & 0xf) === CIGAR_SOFT_CLIP && cigop >> 4 === this.seq_length;
+    _isCGTagPattern(p, numCigarOps) {
+        // htslib stores the placeholder as exactly two ops: <seqlen>S<reflen>N.
+        if (numCigarOps === 2) {
+            const cigop = this._dataView.getInt32(p, true);
+            return (cigop & 0xf) === CIGAR_SOFT_CLIP && cigop >> 4 === this.seq_length;
+        }
+        else {
+            return false;
+        }
     }
     _computeLengthOnRef() {
         const flag_nc = this._dataView.getInt32(this._start + 16, true);
@@ -500,7 +449,7 @@ export default class BamRecord {
         }
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
-        if (this._isCGTagPattern(p)) {
+        if (this._isCGTagPattern(p, numCigarOps)) {
             const cigop2 = this._dataView.getInt32(p + 4, true);
             if ((cigop2 & 0xf) !== CIGAR_REF_SKIP) {
                 console.warn('CG tag with no N tag');
@@ -532,7 +481,7 @@ export default class BamRecord {
         }
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
-        if (this._isCGTagPattern(p)) {
+        if (this._isCGTagPattern(p, numCigarOps)) {
             return (this.tags.CG ??
                 new Uint32Array(0));
         }

package/esm/record.js.map

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

@@ -15,6 +15,14 @@ export interface BamOpts {
     maxInsertSize?: number;
     signal?: AbortSignal;
     filterBy?: FilterBy;
+    /**
+     * Called as the BGZF blocks covering the query are fetched, with cumulative
+     * downloaded bytes and the total to fetch. Reported at block granularity (one
+     * tick per chunk, including instant ticks for cache hits) since chunk byte
+     * sizes are known up front from the index. Lets callers render a determinate
+     * download progress bar.
+     */
+    onProgress?: (bytesDownloaded: number, totalBytes: number) => void;
 }
 export interface BaseOpts {
     signal?: AbortSignal;

package/esm/util.js

@@ -163,8 +163,9 @@ export function applyFilters(records, filterBy) {
     return out;
 }
 // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
-// array if omitted). Records are assumed sorted by start, so we stop scanning
-// at the first record past `max`. Returns the populated array.
+// array if omitted). Records are assumed coordinate-sorted (by ref_id, then
+// start), so we stop scanning once we pass `max` within `chrId` or move past
+// `chrId` entirely. Returns the populated array.
 export function appendInRange(records, chrId, min, max, out = []) {
     for (let i = 0, l = records.length; i < l; i++) {
         const r = records[i];
@@ -176,6 +177,9 @@ export function appendInRange(records, chrId, min, max, out = []) {
                 out.push(r);
             }
         }
+        else if (r.ref_id > chrId) {
+            break;
+        }
     }
     return out;
 }

package/esm/util.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.2.4",
+  "version": "7.3.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {
@@ -46,24 +46,24 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.0.19",
+    "@gmod/bgzf-filehandle": "^6.2.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.1.7"
+    "generic-filehandle2": "^2.1.10"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.8.0",
-    "@vitest/coverage-v8": "^4.1.6",
-    "eslint": "^10.4.0",
+    "@types/node": "^25.9.2",
+    "@vitest/coverage-v8": "^4.1.8",
+    "eslint": "^10.4.1",
     "eslint-plugin-import-x": "^4.16.2",
-    "eslint-plugin-unicorn": "^64.0.0",
+    "eslint-plugin-unicorn": "^65.0.0",
     "prettier": "^3.8.3",
     "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.59.3",
-    "vitest": "^4.1.6"
+    "typescript-eslint": "^8.61.0",
+    "vitest": "^4.1.8"
   },
   "publishConfig": {
     "access": "public"