npm - @gmod/bam - Versions diffs - 7.1.14 → 7.1.16 - Mend

@gmod/bam 7.1.14 → 7.1.16

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 (14) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,10 +1,12 @@
-## [7.1.14](https://github.com/GMOD/bam-js/compare/v7.1.13...v7.1.14) (2025-12-17)
+## [7.1.16](https://github.com/GMOD/bam-js/compare/v7.1.15...v7.1.16) (2026-02-14)
-## [7.1.13](https://github.com/GMOD/bam-js/compare/v7.1.12...v7.1.13) (2025-12-17)
+## [7.1.15](https://github.com/GMOD/bam-js/compare/v7.1.14...v7.1.15) (2025-12-17)
+## [7.1.14](https://github.com/GMOD/bam-js/compare/v7.1.13...v7.1.14) (2025-12-17)
+## [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)

package/dist/bamFile.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import QuickLRU from 'quick-lru';
+import QuickLRU from '@jbrowse/quick-lru';
 import BAI from './bai.ts';
 import Chunk from './chunk.ts';
 import CSI from './csi.ts';

package/dist/bamFile.js CHANGED Viewed

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BAM_MAGIC = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const generic_filehandle2_1 = require("generic-filehandle2");
-const quick_lru_1 = __importDefault(require("quick-lru"));
 const bai_ts_1 = __importDefault(require("./bai.js"));
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));

package/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/record.js CHANGED Viewed

@@ -603,28 +603,28 @@ 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)
+    // inlines flag checks and uses template literal instead of array+join
     get pair_orientation() {
-        if (!this.isSegmentUnmapped() &&
-            !this.isMateUnmapped() &&
-            this.ref_id === this.next_refid) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            return this.template_length > 0
-                ? `${s1}${o1}${s2}${o2}`
-                : `${s2}${o2}${s1}${o1}`;
+        const f = this.flags;
+        // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+        if (f & 0xc || this.ref_id !== this.next_refid) {
+            return undefined;
         }
-        return undefined;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        return this.template_length > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     get bin_mq_nl() {
         return this._dataView.getInt32(this.bytes.start + 12, true);

package/dist/record.js.map CHANGED Viewed

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

@@ -1,4 +1,4 @@
-import QuickLRU from 'quick-lru';
+import QuickLRU from '@jbrowse/quick-lru';
 import BAI from './bai.ts';
 import Chunk from './chunk.ts';
 import CSI from './csi.ts';

package/esm/bamFile.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
+import QuickLRU from '@jbrowse/quick-lru';
 import crc32 from 'crc/calculators/crc32';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
-import QuickLRU from 'quick-lru';
 import BAI from "./bai.js";
 import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/record.js CHANGED Viewed

@@ -598,28 +598,28 @@ 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)
+    // inlines flag checks and uses template literal instead of array+join
     get pair_orientation() {
-        if (!this.isSegmentUnmapped() &&
-            !this.isMateUnmapped() &&
-            this.ref_id === this.next_refid) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            return this.template_length > 0
-                ? `${s1}${o1}${s2}${o2}`
-                : `${s2}${o2}${s1}${o1}`;
+        const f = this.flags;
+        // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+        if (f & 0xc || this.ref_id !== this.next_refid) {
+            return undefined;
         }
-        return undefined;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        return this.template_length > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     get bin_mq_nl() {
         return this._dataView.getInt32(this.bytes.start + 12, true);

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": "7.1.14",
+  "version": "7.1.16",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -50,23 +50,23 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.0.8",
+    "@gmod/bgzf-filehandle": "^6.0.12",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.16"
+    "generic-filehandle2": "^2.0.18"
   },
   "devDependencies": {
-    "@types/node": "^24.10.0",
-    "@vitest/coverage-v8": "^4.0.16",
+    "@types/node": "^25.0.10",
+    "@vitest/coverage-v8": "^4.0.18",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^62.0.0",
-    "prettier": "^3.7.4",
+    "prettier": "^3.8.1",
     "rimraf": "^6.1.2",
     "standard-changelog": "^7.0.1",
     "typescript": "^5.0.4",
-    "typescript-eslint": "^8.49.0",
-    "vitest": "^4.0.16"
+    "typescript-eslint": "^8.54.0",
+    "vitest": "^4.0.18"
   },
   "publishConfig": {
     "access": "public"

package/src/bamFile.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
+import QuickLRU from '@jbrowse/quick-lru'
 import crc32 from 'crc/calculators/crc32'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
-import QuickLRU from 'quick-lru'
 import BAI from './bai.ts'
 import Chunk from './chunk.ts'

package/src/record.ts CHANGED Viewed

@@ -663,30 +663,28 @@ export default class BamRecord {
   }
   // adapted from igv.js
-  // uses template literal instead of array+join (6.4x faster, see benchmarks/string-building.bench.ts)
+  // inlines flag checks and uses template literal instead of array+join
   get pair_orientation() {
-    if (
-      !this.isSegmentUnmapped() &&
-      !this.isMateUnmapped() &&
-      this.ref_id === this.next_refid
-    ) {
-      const s1 = this.isReverseComplemented() ? 'R' : 'F'
-      const s2 = this.isMateReverseComplemented() ? 'R' : 'F'
-      let o1 = ' '
-      let o2 = ' '
-      if (this.isRead1()) {
-        o1 = '1'
-        o2 = '2'
-      } else if (this.isRead2()) {
-        o1 = '2'
-        o2 = '1'
-      }
-      return this.template_length > 0
-        ? `${s1}${o1}${s2}${o2}`
-        : `${s2}${o2}${s1}${o1}`
+    const f = this.flags
+    // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+    if (f & 0xc || this.ref_id !== this.next_refid) {
+      return undefined
     }
-    return undefined
+    const s1 = f & 0x10 ? 'R' : 'F'
+    const s2 = f & 0x20 ? 'R' : 'F'
+    let o1 = ' '
+    let o2 = ' '
+    if (f & 0x40) {
+      o1 = '1'
+      o2 = '2'
+    } else if (f & 0x80) {
+      o1 = '2'
+      o2 = '1'
+    }
+    return this.template_length > 0
+      ? `${s1}${o1}${s2}${o2}`
+      : `${s2}${o2}${s1}${o1}`
   }
   get bin_mq_nl() {