@gmod/bbi - npm Package Compare versions

Comparing version 5.0.1 to 5.0.2

CHANGELOG.md

@@ -0,1 +1,5 @@
+## [5.0.2](https://github.com/GMOD/bbi-js/compare/v5.0.1...v5.0.2) (2024-09-03)
+
+
+
 ## [5.0.1](https://github.com/GMOD/bbi-js/compare/v5.0.0...v5.0.1) (2024-08-09)
@@ -2,0 +6,0 @@

dist/bbi.js

@@ -23,3 +23,3 @@ "use strict";
         if (!this.headerP) {
-            this.headerP = this._getHeader(opts).catch(e => {
+            this.headerP = this._getHeader(opts).catch((e) => {
                 this.headerP = undefined;
@@ -283,3 +283,5 @@ throw e;
                     .readWigData(chrName, start, end, observer, opts)
-                    .catch(e => observer.error(e));
+                    .catch((e) => {
+                    observer.error(e);
+                });
             });
@@ -286,0 +288,0 @@ });

dist/bigbed.js

@@ -215,3 +215,5 @@ "use strict";
                 return new rxjs_1.Observable(observer => {
-                    view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
+                    view.readFeatures(observer, [block], opts).catch((e) => {
+                        observer.error(e);
+                    });
                 }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
@@ -218,0 +220,0 @@ for (const element of x) {

dist/bigwig.js

@@ -31,2 +31,3 @@ "use strict";
                 const zh = zoomLevels[i];
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (zh && zh.reductionLevel <= 2 * basesPerPx) {
@@ -33,0 +34,0 @@ return new block_view_1.BlockView(this.bbi, refsByName, zh.indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');

dist/block-view.js

@@ -23,2 +23,3 @@ "use strict";
 const util_1 = require("./util");
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function coordFilter(s1, e1, s2, e2) {
@@ -167,3 +168,5 @@ return s1 < e2 && e1 >= s2;
                                 if (outstanding === 0) {
-                                    this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request })).catch(e => observer.error(e));
+                                    this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request })).catch((e) => {
+                                        observer.error(e);
+                                    });
                                 }
@@ -204,3 +207,4 @@ }
                 };
-                return cirFobRecur([Number(cirTreeOffset) + 48], 1);
+                cirFobRecur([Number(cirTreeOffset) + 48], 1);
+                return;
             }
@@ -253,2 +257,3 @@ catch (e) {
     parseBigBedBlock(data, startOffset, offset, request) {
+        var _a;
         const items = [];
@@ -273,3 +278,4 @@ let currOffset = startOffset;
             }
-            const rest = data.subarray(currOffset, i).toString();
+            const b = data.subarray(currOffset, i);
+            const rest = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
             currOffset = i + 1;
@@ -276,0 +282,0 @@ items.push({

esm/bbi.js

@@ -11,3 +11,3 @@ import { Buffer } from 'buffer';
         if (!this.headerP) {
-            this.headerP = this._getHeader(opts).catch(e => {
+            this.headerP = this._getHeader(opts).catch((e) => {
                 this.headerP = undefined;
@@ -262,3 +262,5 @@ throw e;
                 .readWigData(chrName, start, end, observer, opts)
-                .catch(e => observer.error(e));
+                .catch((e) => {
+                observer.error(e);
+            });
         });
@@ -265,0 +267,0 @@ }

esm/bigbed.js

@@ -181,3 +181,5 @@ import { Buffer } from 'buffer';
             return new Observable(observer => {
-                view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
+                view.readFeatures(observer, [block], opts).catch((e) => {
+                    observer.error(e);
+                });
             }).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
@@ -184,0 +186,0 @@ for (const element of x) {

esm/bigwig.js

@@ -18,2 +18,3 @@ import { BlockView } from './block-view';
             const zh = zoomLevels[i];
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
@@ -20,0 +21,0 @@ return new BlockView(this.bbi, refsByName, zh.indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');

esm/block-view.js

@@ -8,2 +8,3 @@ import { Buffer } from 'buffer';
 import { groupBlocks, checkAbortSignal } from './util';
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function coordFilter(s1, e1, s2, e2) {
@@ -154,3 +155,5 @@ return s1 < e2 && e1 >= s2;
                                     request,
-                                }).catch(e => observer.error(e));
+                                }).catch((e) => {
+                                    observer.error(e);
+                                });
                             }
@@ -191,3 +194,4 @@ }
             };
-            return cirFobRecur([Number(cirTreeOffset) + 48], 1);
+            cirFobRecur([Number(cirTreeOffset) + 48], 1);
+            return;
         }
@@ -239,2 +243,3 @@ catch (e) {
     parseBigBedBlock(data, startOffset, offset, request) {
+        var _a;
         const items = [];
@@ -259,3 +264,4 @@ let currOffset = startOffset;
             }
-            const rest = data.subarray(currOffset, i).toString();
+            const b = data.subarray(currOffset, i);
+            const rest = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
             currOffset = i + 1;
@@ -262,0 +268,0 @@ items.push({

package.json

 {
   "name": "@gmod/bbi",
-  "version": "5.0.1",
+  "version": "5.0.2",
   "description": "Parser for BigWig/BigBed files",
@@ -23,4 +23,3 @@ "license": "MIT",
   "scripts": {
-    "test": "jest",
-    "coverage": "npm test -- --coverage",
+    "test": "vitest",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0 src",
@@ -33,3 +32,3 @@ "format": "prettier",
     "build": "npm run build:esm && npm run build:es5",
-    "preversion": "npm run lint && npm test && npm run build",
+    "preversion": "npm run lint && npm test run && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
@@ -48,2 +47,3 @@ "postversion": "git push origin master --follow-tags"
     "@gmod/abortable-promise-cache": "^2.0.0",
+    "buffer": "^6.0.3",
     "generic-filehandle": "^3.0.0",
@@ -59,15 +59,13 @@ "pako": "^2.0.0",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^8.0.1",
-    "@typescript-eslint/parser": "^8.0.1",
-    "eslint": "^9.0.0",
-    "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-prettier": "^5.1.3",
+    "@typescript-eslint/eslint-plugin": "^8.4.0",
+    "@typescript-eslint/parser": "^8.4.0",
+    "@vitest/coverage-v8": "^2.0.5",
+    "eslint": "^9.9.1",
     "eslint-plugin-unicorn": "^55.0.0",
-    "jest": "^29.6.2",
-    "jest-environment-jsdom": "^29.6.2",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
-    "ts-jest": "^29.1.2",
-    "typescript": "^5.1.6"
+    "typescript": "^5.1.6",
+    "typescript-eslint": "^8.4.0",
+    "vitest": "^2.0.5"
   },
@@ -74,0 +72,0 @@ "publishConfig": {

src/bbi.ts

@@ -83,3 +83,3 @@ import { Buffer } from 'buffer'
     if (!this.headerP) {
-      this.headerP = this._getHeader(opts).catch(e => {
+      this.headerP = this._getHeader(opts).catch((e: unknown) => {
         this.headerP = undefined
@@ -399,3 +399,5 @@ throw e
         .readWigData(chrName, start, end, observer, opts)
-        .catch(e => observer.error(e))
+        .catch((e: unknown) => {
+          observer.error(e)
+        })
     })
@@ -402,0 +404,0 @@ }

src/bigbed.ts

@@ -235,3 +235,5 @@ import { Buffer } from 'buffer'
       return new Observable<Feature[]>(observer => {
-        view.readFeatures(observer, [block], opts).catch(e => observer.error(e))
+        view.readFeatures(observer, [block], opts).catch((e: unknown) => {
+          observer.error(e)
+        })
       }).pipe(
@@ -238,0 +240,0 @@ reduce((acc, curr) => acc.concat(curr)),

src/bigwig.ts

@@ -21,2 +21,3 @@ import { BlockView } from './block-view'
       const zh = zoomLevels[i]
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (zh && zh.reductionLevel <= 2 * basesPerPx) {
@@ -23,0 +24,0 @@ return new BlockView(

src/block-view.ts

@@ -13,2 +13,5 @@ import { Buffer } from 'buffer'
 
+const decoder =
+  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
+
 interface CoordRequest {
@@ -219,3 +222,5 @@ chrId: number
                   request,
-                }).catch(e => observer.error(e))
+                }).catch((e: unknown) => {
+                  observer.error(e)
+                })
               }
@@ -256,3 +261,4 @@ }
 
-      return cirFobRecur([Number(cirTreeOffset) + 48], 1)
+      cirFobRecur([Number(cirTreeOffset) + 48], 1)
+      return
     } catch (e) {
@@ -338,3 +344,4 @@ observer.error(e)
       }
-      const rest = data.subarray(currOffset, i).toString()
+      const b = data.subarray(currOffset, i)
+      const rest = decoder?.decode(b) ?? b.toString()
       currOffset = i + 1
@@ -341,0 +348,0 @@ items.push({

New alerts

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License

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Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

243451

increased by0.8%

Dev dependency count

15

decreased by-11.76%

Lines of code

3990

increased by0.83%

Worsened metrics

Dependency count

6

increased by20%

Dependency changes

• + Addedbuffer@^6.0.3

• + Addedbase64-js@1.5.1(transitive)

• + Addedbuffer@6.0.3(transitive)

• + Addedieee754@1.2.1(transitive)