npm - @gmod/bam - Versions diffs - 7.1.19 → 7.1.20 - Mend

@gmod/bam 7.1.19 → 7.1.20

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 (44) hide show

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -1,5 +1,10 @@
 // little class representing a chunk in the index
 export default class Chunk {
+    minv;
+    maxv;
+    bin;
+    _fetchedSize;
+    buffer;
     constructor(minv, maxv, bin, _fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;

package/esm/chunk.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;~~IAGxB~~,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
1	+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAA0B;IAEvC,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}

package/esm/csi.js CHANGED Viewed

@@ -13,12 +13,10 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 export default class CSI extends IndexFile {
-    constructor() {
-        super(...arguments);
-        this.maxBinNumber = 0;
-        this.depth = 0;
-        this.minShift = 0;
-    }
+    maxBinNumber = 0;
+    depth = 0;
+    minShift = 0;
+    setupP;
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
         return indexData.indices(refId)?.stats?.lineCount || 0;

package/esm/csi.js.map CHANGED Viewed

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

@@ -32,6 +32,8 @@ async function concat(arr, opts) {
     return concatUint8Array(await Promise.all(res.map(elt => unzip(elt))));
 }
 export default class HtsgetFile extends BamFile {
+    baseUrl;
+    trackId;
     constructor(args) {
         super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;

package/esm/htsget.js.map CHANGED Viewed

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

@@ -1,5 +1,7 @@
 import { optimizeChunks } from "./util.js";
 export default class IndexFile {
+    filehandle;
+    renameRefSeq;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AACA,OAAO,EAAY,cAAc,EAAE,MAAM,WAAW,CAAA;AAUpD,MAAM,CAAC,OAAO,OAAgB,SAAS;~~IAIrC~~,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}
1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AACA,OAAO,EAAY,cAAc,EAAE,MAAM,WAAW,CAAA;AAUpD,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}

package/esm/nullFilehandle.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 export default class NullFilehandle {
-    read(): Promise<any>;
-    stat(): Promise<any>;
-    readFile(): Promise<any>;
-    close(): Promise<any>;
+    read(): Promise<never>;
+    stat(): Promise<never>;
+    readFile(): Promise<never>;
+    close(): Promise<never>;
 }

package/esm/nullIndex.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import IndexFile from './indexFile.ts';
 export default class NullIndex extends IndexFile {
-    lineCount(): Promise<any>;
-    protected _parse(): Promise<any>;
-    indexCov(): Promise<any>;
-    blocksForRange(): Promise<any>;
+    lineCount(): Promise<never>;
+    protected _parse(): Promise<never>;
+    indexCov(): Promise<never>;
+    blocksForRange(): Promise<never>;
 }

package/esm/record.d.ts CHANGED Viewed

@@ -72,6 +72,6 @@ export default class BamRecord {
     get next_pos(): number;
     get template_length(): number;
     seqAt(idx: number): string | undefined;
-    toJSON(): Record<string, any>;
+    toJSON(): Record<string, unknown>;
 }
 export {};

package/esm/record.js CHANGED Viewed

@@ -18,6 +18,17 @@ const ASCII_CIGAR_CODES = [
 // Binary: 0b111001101 = 0x1CD
 const CIGAR_CONSUMES_REF_MASK = 0x1cd;
 export default class BamRecord {
+    fileOffset;
+    bytes;
+    _dataView;
+    _cachedFlags;
+    _cachedRefId;
+    _cachedStart;
+    _cachedEnd;
+    _cachedTags;
+    _cachedCigarAndLength;
+    _cachedNUMERIC_MD;
+    _cachedTagsStart;
     constructor(args) {
         this.bytes = args.bytes;
         this.fileOffset = args.fileOffset;
@@ -608,10 +619,14 @@ export default class BamRecord {
         return buf.join('');
     }
     // adapted from igv.js
-    // uses precomputed lookup table indexed by flag bits + isize sign
+    // uses precomputed lookup table indexed by flag bits + isize sign.
+    // the BAM spec defines tlen as positive for the leftmost segment and
+    // negative for the rightmost, so tlen > 0 reliably indicates which
+    // read comes first without needing position-based correction
+    // (see also: gmod/cram-js src/cramFile/record.ts getPairOrientation)
     get pair_orientation() {
         const f = this.flags;
-        // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+        // unmapped (0x4) or mate unmapped (0x8) -> undefined
         if (f & 0xc || this.ref_id !== this.next_refid) {
             return undefined;
         }

package/esm/record.js.map CHANGED Viewed

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

@@ -1,4 +1,6 @@
 export class VirtualOffset {
+    blockPosition;
+    dataPosition;
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data

package/esm/virtualOffset.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;~~IAGxB~~,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
1	+ {"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/package.json CHANGED Viewed

@@ -1,16 +1,17 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.19",
+  "version": "7.1.20",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
-  "repository": "GMOD/bam-js",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/bam-js.git"
+  },
   "type": "module",
-  "types": "./dist/index.d.ts",
+  "types": "./esm/index.d.ts",
   "exports": {
-    "import": {
-      "import": "./esm/index.js"
-    },
-    "require": {
+    ".": {
+      "import": "./esm/index.js",
       "require": "./dist/index.js"
     }
   },
@@ -20,7 +21,7 @@
     "url": "https://github.com/cmdcolin"
   },
   "engines": {
-    "node": ">=6"
+    "node": ">=20"
   },
   "files": [
     "dist",
@@ -35,11 +36,11 @@
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
     "build:esm": "tsc --outDir esm",
-    "build:es5": "tsc --module commonjs --outDir dist",
-    "build": "yarn build:esm && yarn build:es5",
-    "prebuild": "yarn clean",
+    "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
+    "build": "pnpm build:esm && pnpm build:es5",
+    "prebuild": "pnpm clean",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "yarn lint && yarn test --run && yarn build",
+    "preversion": "pnpm lint && pnpm test --run && pnpm build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
@@ -53,21 +54,21 @@
     "@gmod/bgzf-filehandle": "^6.0.12",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.18"
+    "generic-filehandle2": "^2.1.4"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.3.3",
-    "@vitest/coverage-v8": "^4.0.18",
-    "eslint": "^10.0.2",
-    "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^63.0.0",
+    "@types/node": "^25.5.0",
+    "@vitest/coverage-v8": "^4.1.2",
+    "eslint": "^9.39.4",
+    "eslint-plugin-import": "^2.32.0",
+    "eslint-plugin-unicorn": "^64.0.0",
     "prettier": "^3.8.1",
     "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
-    "typescript": "^5.0.4",
-    "typescript-eslint": "^8.56.1",
-    "vitest": "^4.0.18"
+    "typescript": "^6.0.2",
+    "typescript-eslint": "^8.57.2",
+    "vitest": "^4.1.2"
   },
   "publishConfig": {
     "access": "public"

package/src/nullFilehandle.ts CHANGED Viewed

@@ -1,16 +1,16 @@
 export default class NullFilehandle {
-  public read(): Promise<any> {
+  public read(): Promise<never> {
     throw new Error('never called')
   }
-  public stat(): Promise<any> {
+  public stat(): Promise<never> {
     throw new Error('never called')
   }
-  public readFile(): Promise<any> {
+  public readFile(): Promise<never> {
     throw new Error('never called')
   }
-  public close(): Promise<any> {
+  public close(): Promise<never> {
     throw new Error('never called')
   }
 }

package/src/nullIndex.ts CHANGED Viewed

@@ -1,18 +1,18 @@
 import IndexFile from './indexFile.ts'
 export default class NullIndex extends IndexFile {
-  public lineCount(): Promise<any> {
+  public lineCount(): Promise<never> {
     throw new Error('never called')
   }
-  protected _parse(): Promise<any> {
+  protected _parse(): Promise<never> {
     throw new Error('never called')
   }
-  public async indexCov(): Promise<any> {
+  public async indexCov(): Promise<never> {
     throw new Error('never called')
   }
-  public blocksForRange(): Promise<any> {
+  public blocksForRange(): Promise<never> {
     throw new Error('never called')
   }
 }

package/src/record.ts CHANGED Viewed

@@ -674,10 +674,14 @@ export default class BamRecord {
   }
   // adapted from igv.js
-  // uses precomputed lookup table indexed by flag bits + isize sign
+  // uses precomputed lookup table indexed by flag bits + isize sign.
+  // the BAM spec defines tlen as positive for the leftmost segment and
+  // negative for the rightmost, so tlen > 0 reliably indicates which
+  // read comes first without needing position-based correction
+  // (see also: gmod/cram-js src/cramFile/record.ts getPairOrientation)
   get pair_orientation() {
     const f = this.flags
-    // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+    // unmapped (0x4) or mate unmapped (0x8) -> undefined
     if (f & 0xc || this.ref_id !== this.next_refid) {
       return undefined
     }
@@ -727,7 +731,7 @@ export default class BamRecord {
   }
   toJSON() {
-    const data: Record<string, any> = {}
+    const data: Record<string, unknown> = {}
     for (const k of Object.keys(this)) {
       if (k.startsWith('_') || k === 'bytes') {
         continue