npm - @gmod/bam - Versions diffs - 5.0.1 → 5.0.2 - Mend

@gmod/bam 5.0.1 → 5.0.2

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 (7) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,7 @@
+## [5.0.2](https://github.com/GMOD/bam-js/compare/v5.0.1...v5.0.2) (2024-12-17)
 ## [5.0.1](https://github.com/GMOD/bam-js/compare/v5.0.0...v5.0.1) (2024-12-12)

package/dist/bamFile.js CHANGED Viewed

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BAM_MAGIC = void 0;
-const crc32_1 = __importDefault(require("crc/crc32"));
+const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const generic_filehandle2_1 = require("generic-filehandle2");
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
@@ -344,9 +344,10 @@ class BamFile {
                             (blockStart - dpositions[pos]) +
                             chunk.minv.dataPosition +
                             1
-                        : // must be slice, not subarray for buffer polyfill on web
-                            // @ts-expect-error
-                            crc32_1.default.signed(ba.subarray(blockStart, blockEnd)),
+                        : // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
+                            // internal calculator of crc32 to avoid accidentally importing buffer
+                            // https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
+                            (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
                 });
                 sink.push(feature);
                 if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {

package/dist/bamFile.js.map CHANGED Viewed

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

@@ -1,4 +1,4 @@
-import crc32 from 'crc/crc32';
+import crc32 from 'crc/calculators/crc32';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
@@ -338,9 +338,10 @@ export default class BamFile {
                             (blockStart - dpositions[pos]) +
                             chunk.minv.dataPosition +
                             1
-                        : // must be slice, not subarray for buffer polyfill on web
-                            // @ts-expect-error
-                            crc32.signed(ba.subarray(blockStart, blockEnd)),
+                        : // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
+                            // internal calculator of crc32 to avoid accidentally importing buffer
+                            // https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
+                            crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
                 });
                 sink.push(feature);
                 if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "5.0.1",
+  "version": "5.0.2",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -51,10 +51,7 @@
     "@typescript-eslint/eslint-plugin": "^8.1.0",
     "@typescript-eslint/parser": "^8.1.0",
     "@vitest/coverage-v8": "^2.0.5",
-    "buffer": "^6.0.3",
     "eslint": "^9.9.0",
-    "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-prettier": "^5.1.3",
     "eslint-plugin-unicorn": "^56.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",

package/src/bamFile.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import crc32 from 'crc/crc32'
+import crc32 from 'crc/calculators/crc32'
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle2'
 import AbortablePromiseCache from '@gmod/abortable-promise-cache'
@@ -451,9 +451,10 @@ export default class BamFile {
                 (blockStart - dpositions[pos]) +
                 chunk.minv.dataPosition +
                 1
-              : // must be slice, not subarray for buffer polyfill on web
-                // @ts-expect-error
-                crc32.signed(ba.subarray(blockStart, blockEnd)),
+              : // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
+                // internal calculator of crc32 to avoid accidentally importing buffer
+                // https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
+                crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
         })
         sink.push(feature)