@gmod/tabix 1.5.8 → 1.5.9

package/CHANGELOG.md

@@ -1,3 +1,9 @@
+## [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)
 
 

package/dist/csi.js

@@ -95,7 +95,7 @@ class CSI extends indexFile_1.default {
         const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
         const skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
+        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
         return {
             refIdToName,
             refNameToId,
@@ -198,7 +198,7 @@ class CSI extends indexFile_1.default {
         });
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true));
+        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
         return { lineCount };
     }
     blocksForRange(refName, min, max, opts = {}) {

package/dist/csi.js.map

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

@@ -10,4 +10,5 @@ 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

@@ -1 +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"}
+{"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"}

package/dist/tabixIndexedFile.js

@@ -154,7 +154,7 @@ class TabixIndexedFile {
                     if (n === -1) {
                         break;
                     }
-                    const b = buffer.subarray(blockStart, n);
+                    const b = buffer.slice(blockStart, n);
                     const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
                     if (dpositions) {
                         while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
@@ -244,7 +244,7 @@ class TabixIndexedFile {
                         lastNewline = i;
                     }
                 }
-                bytes = bytes.subarray(0, lastNewline + 1);
+                bytes = bytes.slice(0, lastNewline + 1);
             }
             return bytes;
         });
@@ -400,7 +400,7 @@ class TabixIndexedFile {
         return __awaiter(this, void 0, void 0, function* () {
             const b = Buffer.alloc(size);
             const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
-            return buffer.subarray(0, bytesRead);
+            return buffer.slice(0, bytesRead);
         });
     }
     /**

package/dist/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/dist/tbi.js

@@ -114,7 +114,7 @@ class TabixIndex extends indexFile_1.default {
             const skipLines = bytes.readInt32LE(28);
             // read sequence dictionary
             const nameSectionLength = bytes.readInt32LE(32);
-            const { refNameToId, refIdToName } = this._parseNameBytes(bytes.subarray(36, 36 + nameSectionLength));
+            const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
             // read the indexes for each reference sequence
             let currOffset = 36 + nameSectionLength;
             let firstDataLine;
@@ -180,7 +180,7 @@ class TabixIndex extends indexFile_1.default {
         });
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
+        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {

package/dist/tbi.js.map

@@ -1 +1 @@
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package/esm/csi.js

@@ -54,7 +54,7 @@ export default class CSI extends IndexFile {
         const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
         const skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
+        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
         return {
             refIdToName,
             refNameToId,
@@ -164,7 +164,7 @@ export default class CSI extends IndexFile {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true));
+        const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
         return { lineCount };
     }
     async blocksForRange(refName, min, max, opts = {}) {

package/esm/csi.js.map

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

@@ -1,5 +1,6 @@
 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

@@ -1 +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"}
+{"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,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;AAClB,OAAO,EAAE,gBAAgB,EAAE,GAAG,EAAE,GAAG,EAAE,CAAA"}

package/esm/tabixIndexedFile.js

@@ -139,7 +139,7 @@ export default class TabixIndexedFile {
                 if (n === -1) {
                     break;
                 }
-                const b = buffer.subarray(blockStart, n);
+                const b = buffer.slice(blockStart, n);
                 const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
                 if (dpositions) {
                     while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
@@ -225,7 +225,7 @@ export default class TabixIndexedFile {
                     lastNewline = i;
                 }
             }
-            bytes = bytes.subarray(0, lastNewline + 1);
+            bytes = bytes.slice(0, lastNewline + 1);
         }
         return bytes;
     }
@@ -373,7 +373,7 @@ export default class TabixIndexedFile {
     async _readRegion(pos, size, opts = {}) {
         const b = Buffer.alloc(size);
         const { bytesRead, buffer } = await this.filehandle.read(b, 0, size, pos, opts);
-        return buffer.subarray(0, bytesRead);
+        return buffer.slice(0, bytesRead);
     }
     /**
      * read and uncompress the data in a chunk (composed of one or more

package/esm/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/esm/tbi.js

@@ -74,7 +74,7 @@ export default class TabixIndex extends IndexFile {
         const skipLines = bytes.readInt32LE(28);
         // read sequence dictionary
         const nameSectionLength = bytes.readInt32LE(32);
-        const { refNameToId, refIdToName } = this._parseNameBytes(bytes.subarray(36, 36 + nameSectionLength));
+        const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
         // read the indexes for each reference sequence
         let currOffset = 36 + nameSectionLength;
         let firstDataLine;
@@ -139,7 +139,7 @@ export default class TabixIndex extends IndexFile {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
+        const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {

package/esm/tbi.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",

package/src/csi.ts

@@ -66,7 +66,7 @@ export default class CSI extends IndexFile {
     const nameSectionLength = bytes.readInt32LE(offset + 24)
 
     const { refIdToName, refNameToId } = this._parseNameBytes(
-      bytes.subarray(offset + 28, offset + 28 + nameSectionLength),
+      bytes.slice(offset + 28, offset + 28 + nameSectionLength),
     )
 
     return {
@@ -187,7 +187,7 @@ export default class CSI extends IndexFile {
   parsePseudoBin(bytes: Buffer, offset: number) {
     const lineCount = longToNumber(
       Long.fromBytesLE(
-        bytes.subarray(offset + 28, offset + 36) as unknown as number[],
+        bytes.slice(offset + 28, offset + 36) as unknown as number[],
         true,
       ),
     )

package/src/index.ts

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

package/src/tabixIndexedFile.ts

@@ -203,7 +203,7 @@ export default class TabixIndexedFile {
         if (n === -1) {
           break
         }
-        const b = buffer.subarray(blockStart, n)
+        const b = buffer.slice(blockStart, n)
         const line = decoder?.decode(b) || b.toString()
 
         if (dpositions) {
@@ -311,7 +311,7 @@ export default class TabixIndexedFile {
           lastNewline = i
         }
       }
-      bytes = bytes.subarray(0, lastNewline + 1)
+      bytes = bytes.slice(0, lastNewline + 1)
     }
     return bytes
   }
@@ -482,7 +482,7 @@ export default class TabixIndexedFile {
       opts,
     )
 
-    return buffer.subarray(0, bytesRead)
+    return buffer.slice(0, bytesRead)
   }
 
   /**

package/src/tbi.ts

@@ -83,7 +83,7 @@ export default class TabixIndex extends IndexFile {
     // read sequence dictionary
     const nameSectionLength = bytes.readInt32LE(32)
     const { refNameToId, refIdToName } = this._parseNameBytes(
-      bytes.subarray(36, 36 + nameSectionLength),
+      bytes.slice(36, 36 + nameSectionLength),
     )
 
     // read the indexes for each reference sequence
@@ -155,7 +155,7 @@ export default class TabixIndex extends IndexFile {
   parsePseudoBin(bytes: Buffer, offset: number) {
     const lineCount = longToNumber(
       Long.fromBytesLE(
-        bytes.subarray(offset + 16, offset + 24) as unknown as number[],
+        bytes.slice(offset + 16, offset + 24) as unknown as number[],
         true,
       ),
     )