npm - @gmod/bam - Versions diffs - 7.0.0 → 7.0.1 - Mend

@gmod/bam 7.0.0 → 7.0.1

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 (9) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,7 @@
+## [7.0.1](https://github.com/GMOD/bam-js/compare/v7.0.0...v7.0.1) (2025-11-24)
 # [7.0.0](https://github.com/GMOD/bam-js/compare/v6.1.1...v7.0.0) (2025-11-24)

package/dist/record.d.ts CHANGED Viewed

@@ -61,6 +61,7 @@ export default class BamRecord {
     get num_cigar_ops(): number;
     get read_name_length(): number;
     get num_seq_bytes(): number;
+    get NUMERIC_SEQ(): Uint8Array<ArrayBuffer>;
     get seq(): string;
     get pair_orientation(): string | undefined;
     get bin_mq_nl(): number;

package/dist/record.js CHANGED Viewed

@@ -306,19 +306,24 @@ class BamRecord {
     get num_seq_bytes() {
         return (this.seq_length + 1) >> 1;
     }
-    get seq() {
+    get NUMERIC_SEQ() {
         const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
+        const seqBytes = this.byteArray.slice(p, p + this.num_seq_bytes);
+        return new Uint8Array(seqBytes.buffer, seqBytes.byteOffset, this.num_seq_bytes);
+    }
+    get seq() {
+        const numeric = this.NUMERIC_SEQ;
         const len = this.seq_length;
         const buf = new Array(len);
         let i = 0;
         const fullBytes = len >> 1;
         for (let j = 0; j < fullBytes; ++j) {
-            const sb = this.byteArray[p + j];
+            const sb = numeric[j];
             buf[i++] = SEQRET_DECODER[(sb & 0xf0) >> 4];
             buf[i++] = SEQRET_DECODER[sb & 0x0f];
         }
         if (i < len) {
-            const sb = this.byteArray[p + fullBytes];
+            const sb = numeric[fullBytes];
             buf[i] = SEQRET_DECODER[(sb & 0xf0) >> 4];
         }
         return buf.join('');

package/dist/record.js.map CHANGED Viewed

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

@@ -61,6 +61,7 @@ export default class BamRecord {
     get num_cigar_ops(): number;
     get read_name_length(): number;
     get num_seq_bytes(): number;
+    get NUMERIC_SEQ(): Uint8Array<ArrayBuffer>;
     get seq(): string;
     get pair_orientation(): string | undefined;
     get bin_mq_nl(): number;

package/esm/record.js CHANGED Viewed

@@ -301,19 +301,24 @@ export default class BamRecord {
     get num_seq_bytes() {
         return (this.seq_length + 1) >> 1;
     }
-    get seq() {
+    get NUMERIC_SEQ() {
         const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
+        const seqBytes = this.byteArray.slice(p, p + this.num_seq_bytes);
+        return new Uint8Array(seqBytes.buffer, seqBytes.byteOffset, this.num_seq_bytes);
+    }
+    get seq() {
+        const numeric = this.NUMERIC_SEQ;
         const len = this.seq_length;
         const buf = new Array(len);
         let i = 0;
         const fullBytes = len >> 1;
         for (let j = 0; j < fullBytes; ++j) {
-            const sb = this.byteArray[p + j];
+            const sb = numeric[j];
             buf[i++] = SEQRET_DECODER[(sb & 0xf0) >> 4];
             buf[i++] = SEQRET_DECODER[sb & 0x0f];
         }
         if (i < len) {
-            const sb = this.byteArray[p + fullBytes];
+            const sb = numeric[fullBytes];
             buf[i] = SEQRET_DECODER[(sb & 0xf0) >> 4];
         }
         return buf.join('');

package/esm/record.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.0.0",
+  "version": "7.0.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -39,7 +39,7 @@
     "build": "yarn build:esm && yarn build:es5",
     "prebuild": "yarn clean",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "yarn lint && npm test --run && yarn build",
+    "preversion": "yarn lint && yarn test --run && yarn build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },

package/src/record.ts CHANGED Viewed

@@ -357,21 +357,27 @@ export default class BamRecord {
     return (this.seq_length + 1) >> 1
   }
-  get seq() {
+  get NUMERIC_SEQ() {
     const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4
+    const seqBytes = this.byteArray.slice(p, p + this.num_seq_bytes)
+    return new Uint8Array(seqBytes.buffer, seqBytes.byteOffset, this.num_seq_bytes)
+  }
+  get seq() {
+    const numeric = this.NUMERIC_SEQ
     const len = this.seq_length
     const buf = new Array(len)
     let i = 0
     const fullBytes = len >> 1
     for (let j = 0; j < fullBytes; ++j) {
-      const sb = this.byteArray[p + j]!
+      const sb = numeric[j]!
       buf[i++] = SEQRET_DECODER[(sb & 0xf0) >> 4]
       buf[i++] = SEQRET_DECODER[sb & 0x0f]
     }
     if (i < len) {
-      const sb = this.byteArray[p + fullBytes]!
+      const sb = numeric[fullBytes]!
       buf[i] = SEQRET_DECODER[(sb & 0xf0) >> 4]
     }