npm - @gmod/tabix - Versions diffs - 1.5.9 → 1.5.11 - Mend

@gmod/tabix 1.5.9 → 1.5.11

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 (34) hide show

package/CHANGELOG.md +14 -3
package/dist/csi.d.ts +1 -0
package/dist/csi.js.map +1 -1
package/dist/index.js +0 -1
package/dist/index.js.map +1 -1
package/dist/tabixIndexedFile.d.ts +1 -0
package/dist/tabixIndexedFile.js +2 -1
package/dist/tabixIndexedFile.js.map +1 -1
package/dist/tbi.d.ts +1 -0
package/dist/tbi.js.map +1 -1
package/dist/util.js +0 -4
package/dist/util.js.map +1 -1
package/dist/virtualOffset.d.ts +1 -0
package/dist/virtualOffset.js.map +1 -1
package/esm/csi.d.ts +1 -0
package/esm/csi.js.map +1 -1
package/esm/index.js +0 -1
package/esm/index.js.map +1 -1
package/esm/tabixIndexedFile.d.ts +1 -0
package/esm/tabixIndexedFile.js +1 -0
package/esm/tabixIndexedFile.js.map +1 -1
package/esm/tbi.d.ts +1 -0
package/esm/tbi.js.map +1 -1
package/esm/util.js +0 -4
package/esm/util.js.map +1 -1
package/esm/virtualOffset.d.ts +1 -0
package/esm/virtualOffset.js.map +1 -1
package/package.json +8 -9
package/src/csi.ts +1 -0
package/src/index.ts +0 -1
package/src/tabixIndexedFile.ts +1 -0
package/src/tbi.ts +1 -0
package/src/util.ts +0 -4
package/src/virtualOffset.ts +1 -0

package/CHANGELOG.md CHANGED Viewed

@@ -1,12 +1,23 @@
-## [1.5.9](https://github.com/GMOD/tabix-js/compare/v1.5.8...v1.5.9) (2023-03-27)
+## [1.5.11](https://github.com/GMOD/tabix-js/compare/v1.5.10...v1.5.11) (2023-07-10)
+### Features
-- Revert the Buffer::slice -> Buffer::subarray change due to use with polyfills
+* explicit buffer import ([#140](https://github.com/GMOD/tabix-js/issues/140)) ([fb80ac8](https://github.com/GMOD/tabix-js/commit/fb80ac813a0d40255556de3ab28dae1940f59c1d))
-## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
+- Add explicit buffer import
+## [1.5.10](https://github.com/GMOD/tabix-js/compare/v1.5.9...v1.5.10) (2023-03-30)
+- Remove stray console.log
+## [1.5.9](https://github.com/GMOD/tabix-js/compare/v1.5.8...v1.5.9) (2023-03-27)
+- Revert the Buffer::slice -> Buffer::subarray change due to use with polyfills
+## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
 - Make yieldTime optional

package/dist/csi.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';

package/dist/csi.js.map CHANGED Viewed

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

@@ -10,5 +10,4 @@ const tbi_1 = __importDefault(require("./tbi"));
 exports.TBI = tbi_1.default;
 const csi_1 = __importDefault(require("./csi"));
 exports.CSI = csi_1.default;
-console.log('ret');
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAAiD;~~AAKxC~~,~~2BALF~~,0BAAgB,~~CAKE~~;~~AAJzB~~,gDAAuB;~~AAII~~,~~cAJpB~~,aAAG,~~CAIoB~~;~~AAH9B~~,gDAAuB;~~AAGS~~,~~cAHzB~~,aAAG,~~CAGyB;AADnC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA~~"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAAiD;AAIxC,2BAJF,0BAAgB,CAIE;AAHzB,gDAAuB;AAGI,cAHpB,aAAG,CAGoB;AAF9B,gDAAuB;AAES,cAFzB,aAAG,CAEyB"}

package/dist/tabixIndexedFile.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options, IndexData } from './indexFile';
 import Chunk from './chunk';

package/dist/tabixIndexedFile.js CHANGED Viewed

@@ -14,6 +14,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
+const buffer_1 = require("buffer");
 const generic_filehandle_1 = require("generic-filehandle");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("./util");
@@ -398,7 +399,7 @@ class TabixIndexedFile {
     }
     _readRegion(pos, size, opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
-            const b = Buffer.alloc(size);
+            const b = buffer_1.Buffer.alloc(size);
             const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
             return buffer.slice(0, bytesRead);
         });

package/dist/tabixIndexedFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/tbi.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';

package/dist/tbi.js.map CHANGED Viewed

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

@@ -36,7 +36,6 @@ function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        // console.log('bam aborted!')
         if (typeof DOMException !== 'undefined') {
             // eslint-disable-next-line  no-undef
             throw new DOMException('aborted', 'AbortError');
@@ -100,9 +99,6 @@ function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-        // else {
-        //   console.log(`skipping chunk ${chunk}`)
-        // }
     });
     return mergedChunks;
 }

package/dist/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/virtualOffset.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 export default class VirtualOffset {
     blockPosition: number;
     dataPosition: number;

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package/esm/csi.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';

package/esm/csi.js.map CHANGED Viewed

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

@@ -1,6 +1,5 @@
 import TabixIndexedFile from './tabixIndexedFile';
 import TBI from './tbi';
 import CSI from './csi';
-console.log('ret');
 export { TabixIndexedFile, TBI, CSI };
 //# sourceMappingURL=index.js.map

package/esm/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,OAAO,EAAE,gBAAgB,EAAE,GAAG,EAAE,GAAG,EAAE,CAAA"}

package/esm/tabixIndexedFile.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options, IndexData } from './indexFile';
 import Chunk from './chunk';

package/esm/tabixIndexedFile.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import AbortablePromiseCache from 'abortable-promise-cache';
 import LRU from 'quick-lru';
+import { Buffer } from 'buffer';
 import { LocalFile } from 'generic-filehandle';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { checkAbortSignal } from './util';

package/esm/tabixIndexedFile.js.map CHANGED Viewed

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

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';

package/esm/tbi.js.map CHANGED Viewed

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package/esm/util.js CHANGED Viewed

@@ -23,7 +23,6 @@ export function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        // console.log('bam aborted!')
         if (typeof DOMException !== 'undefined') {
             // eslint-disable-next-line  no-undef
             throw new DOMException('aborted', 'AbortError');
@@ -82,9 +81,6 @@ export function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-        // else {
-        //   console.log(`skipping chunk ${chunk}`)
-        // }
     });
     return mergedChunks;
 }

package/esm/util.js.map CHANGED Viewed

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

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 export default class VirtualOffset {
     blockPosition: number;
     dataPosition: number;

package/esm/virtualOffset.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.9",
+  "version": "1.5.11",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -49,20 +49,19 @@
     "@types/jest": "^29.5.0",
     "@types/long": "^4.0.0",
     "@types/node": "^18.15.5",
-    "@types/quick-lru": "2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.56.0",
-    "@typescript-eslint/parser": "^5.56.0",
-    "eslint": "^8.36.0",
+    "@typescript-eslint/eslint-plugin": "^5.59.6",
+    "@typescript-eslint/parser": "^5.59.6",
+    "eslint": "^8.40.0",
     "eslint-config-prettier": "^8.8.0",
     "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^4.2.1",
     "jest": "^29.5.0",
     "jest-environment-jsdom": "^29.5.0",
-    "prettier": "^2.8.6",
-    "rimraf": "^4.4.1",
+    "prettier": "^2.8.8",
+    "rimraf": "^5.0.1",
     "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.0.5",
-    "typescript": "^5.0.2"
+    "ts-jest": "^29.1.0",
+    "typescript": "^5.0.4"
   },
   "publishConfig": {
     "access": "public"

package/src/csi.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 import Long from 'long'
+import { Buffer } from 'buffer'
 import { unzip } from '@gmod/bgzf-filehandle'
 import VirtualOffset, { fromBytes } from './virtualOffset'

package/src/index.ts CHANGED Viewed

@@ -2,5 +2,4 @@ import TabixIndexedFile from './tabixIndexedFile'
 import TBI from './tbi'
 import CSI from './csi'
-console.log('ret')
 export { TabixIndexedFile, TBI, CSI }

package/src/tabixIndexedFile.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 import AbortablePromiseCache from 'abortable-promise-cache'
 import LRU from 'quick-lru'
+import { Buffer } from 'buffer'
 import { GenericFilehandle, LocalFile } from 'generic-filehandle'
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
 import { checkAbortSignal } from './util'

package/src/tbi.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 import Long from 'long'
+import { Buffer } from 'buffer'
 import VirtualOffset, { fromBytes } from './virtualOffset'
 import Chunk from './chunk'
 import { unzip } from '@gmod/bgzf-filehandle'

package/src/util.ts CHANGED Viewed

@@ -31,7 +31,6 @@ export function checkAbortSignal(signal?: AbortSignal) {
   }
   if (signal.aborted) {
-    // console.log('bam aborted!')
     if (typeof DOMException !== 'undefined') {
       // eslint-disable-next-line  no-undef
       throw new DOMException('aborted', 'AbortError')
@@ -94,9 +93,6 @@ export function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset) {
         }
       }
     }
-    // else {
-    //   console.log(`skipping chunk ${chunk}`)
-    // }
   })
   return mergedChunks

package/src/virtualOffset.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer'
 export default class VirtualOffset {
   public blockPosition: number
   public dataPosition: number