npm - @gmod/cram - Versions diffs - 1.7.2 → 1.7.4 - Mend

@gmod/cram 1.7.2 → 1.7.4

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 (22) hide show

package/CHANGELOG.md +9 -0
package/dist/cram-bundle.js +1 -1
package/dist/cram-bundle.js.LICENSE.txt +1 -1
package/dist/cramFile/file.js +5 -3
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.d.ts +1 -1
package/dist/cramFile/record.js +2 -3
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +5 -1
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/file.js +2 -0
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.d.ts +1 -1
package/esm/cramFile/record.js +2 -3
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +5 -1
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/package.json +5 -6
package/src/cramFile/file.ts +2 -0
package/src/cramFile/record.ts +2 -3
package/src/cramFile/slice/decodeRecord.ts +5 -1
package/src/typings/bzip2.d.ts +0 -7

package/dist/cram-bundle.js.LICENSE.txt CHANGED Viewed

@@ -12,6 +12,6 @@
  * @license  MIT
  */
-/*! https://mths.be/punycode v1.3.2 by @mathias */
+/*! https://mths.be/punycode v1.4.1 by @mathias */
 /*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */

package/dist/cramFile/file.js CHANGED Viewed

@@ -15,6 +15,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const unzip_1 = require("../unzip");
 const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
+// @ts-expect-error
+const bzip2_1 = __importDefault(require("bzip2"));
 const errors_1 = require("../errors");
 const rans_1 = __importDefault(require("../rans"));
 const sectionParsers_1 = require("./sectionParsers");
@@ -256,12 +258,12 @@ class CramFile {
             result.copy(outputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
-            const bits = bzip2.array(inputBuffer);
-            let size = bzip2.header(bits);
+            const bits = bzip2_1.default.array(inputBuffer);
+            let size = bzip2_1.default.header(bits);
             let j = 0;
             let chunk;
             do {
-                chunk = bzip2.decompress(bits, size);
+                chunk = bzip2_1.default.decompress(bits, size);
                 if (chunk != -1) {
                     Buffer.from(chunk).copy(outputBuffer, j);
                     j += chunk.length;

package/dist/cramFile/file.js.map CHANGED Viewed

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

@@ -107,7 +107,7 @@ export default class CramRecord {
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
-     * subsitution read features given the actual substituted and reference
+     * substitution read features given the actual substituted and reference
      * base pairs, and will make the `getReadSequence()` method work.
      *
      * @param {object} refRegion

package/dist/cramFile/record.js CHANGED Viewed

@@ -34,8 +34,7 @@ function decodeReadSequence(cramRecord, refRegion) {
                 currentReadFeature += 1;
                 if (feature.code === 'b') {
                     // specify a base pair for some reason
-                    const ret = feature.data.split(',');
-                    const added = String.fromCharCode(...ret);
+                    const added = feature.data;
                     bases += added;
                     regionPos += added.length;
                 }
@@ -337,7 +336,7 @@ class CramRecord {
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
-     * subsitution read features given the actual substituted and reference
+     * substitution read features given the actual substituted and reference
      * base pairs, and will make the `getReadSequence()` method work.
      *
      * @param {object} refRegion

package/dist/cramFile/record.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -120,7 +120,11 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
             return String.fromCharCode(data);
         }
         if (type === 'string') {
-            return data.toString('utf8');
+            let r = '';
+            for (let i = 0; i < data.byteLength; i++) {
+                r += String.fromCharCode(data[i]);
+            }
+            return r;
         }
         if (type === 'numArray') {
             return data.toArray();

package/dist/cramFile/slice/decodeRecord.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/cramFile/file.js CHANGED Viewed

@@ -1,6 +1,8 @@
 import { unzip } from '../unzip';
 import crc32 from 'buffer-crc32';
 import QuickLRU from 'quick-lru';
+// @ts-expect-error
+import bzip2 from 'bzip2';
 import { CramMalformedError, CramUnimplementedError } from '../errors';
 import ransuncompress from '../rans';
 import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';

package/esm/cramFile/file.js.map CHANGED Viewed

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

@@ -107,7 +107,7 @@ export default class CramRecord {
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
-     * subsitution read features given the actual substituted and reference
+     * substitution read features given the actual substituted and reference
      * base pairs, and will make the `getReadSequence()` method work.
      *
      * @param {object} refRegion

package/esm/cramFile/record.js CHANGED Viewed

@@ -28,8 +28,7 @@ function decodeReadSequence(cramRecord, refRegion) {
                 currentReadFeature += 1;
                 if (feature.code === 'b') {
                     // specify a base pair for some reason
-                    const ret = feature.data.split(',');
-                    const added = String.fromCharCode(...ret);
+                    const added = feature.data;
                     bases += added;
                     regionPos += added.length;
                 }
@@ -331,7 +330,7 @@ export default class CramRecord {
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
-     * subsitution read features given the actual substituted and reference
+     * substitution read features given the actual substituted and reference
      * base pairs, and will make the `getReadSequence()` method work.
      *
      * @param {object} refRegion

package/esm/cramFile/record.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -115,7 +115,11 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
             return String.fromCharCode(data);
         }
         if (type === 'string') {
-            return data.toString('utf8');
+            let r = '';
+            for (let i = 0; i < data.byteLength; i++) {
+                r += String.fromCharCode(data[i]);
+            }
+            return r;
         }
         if (type === 'numArray') {
             return data.toArray();

package/esm/cramFile/slice/decodeRecord.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.7.2",
+  "version": "1.7.4",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -47,7 +47,6 @@
     "abortable-promise-cache": "^1.2.0",
     "buffer-crc32": "^0.2.13",
     "bzip2": "^0.1.1",
-    "cross-fetch": "^3.0.0",
     "long": "^4.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
@@ -70,15 +69,15 @@
     "eslint-config-prettier": "^8.5.0",
     "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^4.0.0",
-    "glob": "^8.0.3",
+    "glob": "^10.3.1",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
+    "rimraf": "^5.0.1",
     "ts-jest": "^29.0.3",
-    "typescript": "^4.9.4",
+    "typescript": "^5.0.3",
     "url": "^0.11.0",
-    "webpack": "5.75.0",
+    "webpack": "5.88.1",
     "webpack-cli": "^5.0.1"
   },
   "publishConfig": {

package/src/cramFile/file.ts CHANGED Viewed

@@ -1,6 +1,8 @@
 import { unzip } from '../unzip'
 import crc32 from 'buffer-crc32'
 import QuickLRU from 'quick-lru'
+// @ts-expect-error
+import bzip2 from 'bzip2'
 import { CramMalformedError, CramUnimplementedError } from '../errors'
 import ransuncompress from '../rans'

package/src/cramFile/record.ts CHANGED Viewed

@@ -54,8 +54,7 @@ function decodeReadSequence(
         if (feature.code === 'b') {
           // specify a base pair for some reason
-          const ret = feature.data.split(',')
-          const added = String.fromCharCode(...ret)
+          const added = feature.data
           bases += added
           regionPos += added.length
         } else if (feature.code === 'B') {
@@ -451,7 +450,7 @@ export default class CramRecord {
   /**
    * Annotates this feature with the given reference sequence basepair
    * information. This will add a `sub` and a `ref` item to base
-   * subsitution read features given the actual substituted and reference
+   * substitution read features given the actual substituted and reference
    * base pairs, and will make the `getReadSequence()` method work.
    *
    * @param {object} refRegion

package/src/cramFile/slice/decodeRecord.ts CHANGED Viewed

@@ -141,7 +141,11 @@ function decodeReadFeatures(
       return String.fromCharCode(data)
     }
     if (type === 'string') {
-      return data.toString('utf8')
+      let r = ''
+      for (let i = 0; i < data.byteLength; i++) {
+        r += String.fromCharCode(data[i])
+      }
+      return r
     }
     if (type === 'numArray') {
       return data.toArray()

package/src/typings/bzip2.d.ts DELETED Viewed

@@ -1,7 +0,0 @@
-declare type BitReader = { __type: void }
-declare const bzip2: {
-  array: (buffer: Buffer) => BitReader
-  header: (reader: BitReader) => number
-  decompress: (reader: BitReader, size: number, length?: number) => -1 | string
-}