@gmod/bbi - npm Package Compare versions

Comparing version 2.0.5 to 3.0.0

CHANGELOG.md

@@ -1,5 +0,9 @@
-## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
+# [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
 
 
 
+- Update to rxjs 7
+
+## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
+
 - Cleanup package.json and README
@@ -9,4 +13,2 @@
 
-
-
 - Use plain TextDecoder for decoding autoSql
@@ -13,0 +15,0 @@

dist/bbi.js

@@ -81,2 +81,16 @@ "use strict";
 class BBI {
+    /* fetch and parse header information from a bigwig or bigbed file
+     * @param abortSignal - abort the operation, can be null
+     * @return a Header object
+     */
+    getHeader(opts = {}) {
+        const options = 'aborted' in opts ? { signal: opts } : opts;
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     /*
@@ -104,16 +118,2 @@ * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
     }
-    /* fetch and parse header information from a bigwig or bigbed file
-     * @param abortSignal - abort the operation, can be null
-     * @return a Header object
-     */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
-                this.headerP = undefined;
-                throw e;
-            });
-        }
-        return this.headerP;
-    }
     _getHeader(opts) {
@@ -275,6 +275,4 @@ return __awaiter(this, void 0, void 0, function* () {
             const ob = yield this.getFeatureStream(refName, start, end, opts);
-            const ret = yield ob
-                .pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)))
-                .toPromise();
-            return ret || [];
+            const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
+            return ret.flat();
         });
@@ -281,0 +279,0 @@ }

dist/bigbed.js

@@ -197,3 +197,3 @@ "use strict";
             });
-            const ret = yield (0, rxjs_1.merge)(...res).toPromise();
+            const ret = yield (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
             return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
@@ -200,0 +200,0 @@ });

esm/bbi.js

 import { Parser } from 'binary-parser';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import { reduce } from 'rxjs/operators';
+import { firstValueFrom, Observable } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import { BlockView } from './blockView';
@@ -69,2 +69,16 @@ const BIG_WIG_MAGIC = -2003829722;
 export class BBI {
+    /* fetch and parse header information from a bigwig or bigbed file
+     * @param abortSignal - abort the operation, can be null
+     * @return a Header object
+     */
+    getHeader(opts = {}) {
+        const options = 'aborted' in opts ? { signal: opts } : opts;
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     /*
@@ -92,16 +106,2 @@ * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
     }
-    /* fetch and parse header information from a bigwig or bigbed file
-     * @param abortSignal - abort the operation, can be null
-     * @return a Header object
-     */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
-                this.headerP = undefined;
-                throw e;
-            });
-        }
-        return this.headerP;
-    }
     async _getHeader(opts) {
@@ -252,8 +252,6 @@ const header = await this._getMainHeader(opts);
         const ob = await this.getFeatureStream(refName, start, end, opts);
-        const ret = await ob
-            .pipe(reduce((acc, curr) => acc.concat(curr)))
-            .toPromise();
-        return ret || [];
+        const ret = await firstValueFrom(ob.pipe(toArray()));
+        return ret.flat();
     }
 }
 //# sourceMappingURL=bbi.js.map

esm/bigbed.js

 import { Parser } from 'binary-parser';
-import { Observable, merge } from 'rxjs';
+import { Observable, merge, firstValueFrom } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
@@ -174,3 +174,3 @@ import AbortablePromiseCache from 'abortable-promise-cache';
         });
-        const ret = await merge(...res).toPromise();
+        const ret = await firstValueFrom(merge(...res));
         return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
@@ -177,0 +177,0 @@ }

package.json

 {
   "name": "@gmod/bbi",
-  "version": "2.0.5",
+  "version": "3.0.0",
   "description": "Parser for BigWig/BigBed files",
@@ -49,24 +49,24 @@ "license": "MIT",
     "quick-lru": "^4.0.0",
-    "rxjs": "^6.5.2"
+    "rxjs": "^7.8.0"
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.1.2",
+    "@types/jest": "^29.2.4",
     "@types/long": "^5.0.0",
-    "@types/node": "^18.11.0",
+    "@types/node": "^18.11.15",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.40.0",
-    "@typescript-eslint/parser": "^5.40.0",
+    "@typescript-eslint/eslint-plugin": "^5.46.1",
+    "@typescript-eslint/parser": "^5.46.1",
     "cross-fetch": "^3.0.2",
-    "eslint": "^8.25.0",
+    "eslint": "^8.29.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^29.2.0",
-    "jest-environment-jsdom": "^29.2.0",
-    "prettier": "^2.5.1",
+    "jest": "^29.3.1",
+    "jest-environment-jsdom": "^29.3.1",
+    "prettier": "^2.8.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.11",
     "ts-jest": "^29.0.3",
-    "typescript": "^4.8.4"
+    "typescript": "^4.9.4"
   },
@@ -73,0 +73,0 @@ "publishConfig": {

README.md

@@ -13,10 +13,12 @@ # bbi-js
 
-    const {BigWig} = require('@gmod/bbi');
-    const file = new BigWig({
-      path: 'volvox.bw'
-    });
-    (async () => {
-      await file.getHeader();
-      const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 });
-    })();
+```ts
+const { BigWig } = require('@gmod/bbi')
+const file = new BigWig({
+  path: 'volvox.bw',
+})
+;(async () => {
+  await file.getHeader()
+  const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
+})()
+```
 
@@ -26,22 +28,23 @@ If using remotely, you can use it in combination with generic-filehandle or your own implementation of something like generic-filehandle
 
-    const {BigWig} = require('@gmod/bbi');
-    const {RemoteFile} = require('generic-filehandle')
+```ts
+const { BigWig } = require('@gmod/bbi')
+const { RemoteFile } = require('generic-filehandle')
 
-    // if running in the browser, RemoteFile will use the the global fetch
-    const file = new BigWig({
-      filehandle: new RemoteFile('volvox.bw')
-    });
+// if running in the browser, RemoteFile will use the the global fetch
+const file = new BigWig({
+  filehandle: new RemoteFile('volvox.bw'),
+})
 
+// if running under node.js you must supply the fetch function to RemoteFile
+const fetch = require('node-fetch')
+const file = new BigWig({
+  filehandle: new RemoteFile('volvox.bw', { fetch }),
+})
 
-    // if running under node.js you must supply the fetch function to RemoteFile
-    const fetch = require('node-fetch')
-    const file = new BigWig({
-      filehandle: new RemoteFile('volvox.bw', {fetch})
-    });
+;(async () => {
+  await file.getHeader()
+  const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
+})()
+```
 
-    (async () => {
-      await file.getHeader();
-      const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 });
-    })();
-
 ## Documentation
@@ -72,7 +75,9 @@
 
-    const feats = await bigwig.getFeatures('chr1', 0, 100)
-    // returns array of features with start, end, score
-    // coordinates on returned data are are 0-based half open
-    // no conversion to 1-based as in wig is done)
-    // note refseq is not returned on the object, it is clearly chr1 from the query though
+```ts
+const feats = await bigwig.getFeatures('chr1', 0, 100)
+// returns array of features with start, end, score
+// coordinates on returned data are are 0-based half open
+// no conversion to 1-based as in wig is done)
+// note refseq is not returned on the object, it is clearly chr1 from the query though
+```
 
@@ -95,10 +100,16 @@ ### Understanding scale and reductionLevel
 
-    const observer = await bigwig.getFeatureStream('chr1', 0, 100)
-    observer.subscribe(chunk => {
-       /* chunk contains array of features with start, end, score */
-    }, error => {
-       /* process error */
-    }, () => {
-       /* completed */
-    })
+```ts
+const observer = await bigwig.getFeatureStream('chr1', 0, 100)
+observer.subscribe(
+  chunk => {
+    /* chunk contains array of features with start, end, score */
+  },
+  error => {
+    /* process error */
+  },
+  () => {
+    /* completed */
+  },
+)
+```
 
@@ -135,19 +146,19 @@ ### BigBed
 
-```js
-    import {BigBed} from '@gmod/bbi'
-    import BED from '@gmod/bed'
+```ts
+import {BigBed} from '@gmod/bbi'
+import BED from '@gmod/bed'
 
-    const ti = new BigBed({
-      filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
-    })
-    const {autoSql} = await ti.getHeader()
-    const feats = await ti.getFeatures('chr7', 0, 100000)
-    const parser = new BED({autoSql})
-    const lines = feats.map(f => {
-        const { start, end, rest, uniqueId } = f
-        return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
-    })
-    // @gmod/bbi returns features with {uniqueId, start, end, rest}
-    // we reconstitute this as a line for @gmod/bed with a template string
-    // note: the uniqueId is based on file offsets and helps to deduplicate exact feature copies if they exist
+const ti = new BigBed({
+  filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
+})
+const {autoSql} = await ti.getHeader()
+const feats = await ti.getFeatures('chr7', 0, 100000)
+const parser = new BED({autoSql})
+const lines = feats.map(f => {
+    const { start, end, rest, uniqueId } = f
+    return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
+})
+// @gmod/bbi returns features with {uniqueId, start, end, rest}
+// we reconstitute this as a line for @gmod/bed with a template string
+// note: the uniqueId is based on file offsets and helps to deduplicate exact feature copies if they exist
 ```
@@ -157,25 +168,29 @@
 
+```json
+{
+  "chromId": 0,
+  "start": 64068,
+  "end": 64107,
+  "rest": "uc003sil.1\t0\t-\t64068\t64068\t255,0,0\t.\tDQ584609",
+  "uniqueId": "bb-171"
+}
 ```
-      { chromId: 0,
-        start: 64068,
-        end: 64107,
-        rest: 'uc003sil.1\t0\t-\t64068\t64068\t255,0,0\t.\tDQ584609',
-        uniqueId: 'bb-171' }
-```
 
 Features after parsing with @gmod/bed:
 
+```json
+{
+  "uniqueId": "bb-0",
+  "chrom": "chr7",
+  "chromStart": 54028,
+  "chromEnd": 73584,
+  "name": "uc003sii.2",
+  "score": 0,
+  "strand": -1,
+  "thickStart": 54028,
+  "thickEnd": 54028,
+  "reserved": "255,0,0",
+  "spID": "AL137655"
+}
 ```
-      { uniqueId: 'bb-0',
-        chrom: 'chr7',
-        chromStart: 54028,
-        chromEnd: 73584,
-        name: 'uc003sii.2',
-        score: 0,
-        strand: -1,
-        thickStart: 54028,
-        thickEnd: 54028,
-        reserved: '255,0,0',
-        spID: 'AL137655' }
-```
 
@@ -182,0 +197,0 @@ ## Academic Use

src/bbi.ts

 import { Parser } from 'binary-parser'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
-import { Observable, Observer } from 'rxjs'
-import { reduce } from 'rxjs/operators'
+import { firstValueFrom, Observable, Observer } from 'rxjs'
+import { toArray } from 'rxjs/operators'
 import { BlockView } from './blockView'
@@ -370,10 +370,8 @@
     },
-  ): Promise<Feature[]> {
+  ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)
 
-    const ret = await ob
-      .pipe(reduce((acc, curr) => acc.concat(curr)))
-      .toPromise()
-    return ret || []
+    const ret = await firstValueFrom(ob.pipe(toArray()))
+    return ret.flat()
   }
 }

src/bigbed.ts

 import { Parser } from 'binary-parser'
-import { Observable, merge } from 'rxjs'
+import { Observable, merge, firstValueFrom } from 'rxjs'
 import { map, reduce } from 'rxjs/operators'
@@ -219,6 +219,3 @@ import AbortablePromiseCache from 'abortable-promise-cache'
    */
-  public async searchExtraIndex(
-    name: string,
-    opts: RequestOptions = {},
-  ): Promise<Feature[]> {
+  public async searchExtraIndex(name: string, opts: RequestOptions = {}) {
     const blocks = await this.searchExtraIndexBlocks(name, opts)
@@ -242,5 +239,5 @@ if (!blocks.length) {
     })
-    const ret = await merge(...res).toPromise()
+    const ret = await firstValueFrom(merge(...res))
     return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name)
   }
 }

No alert changes

Improved metrics

Total package byte prevSize

252831

increased by3.05%

Number of package files

83

increased by1.22%

Number of lines in readme file

198

increased by8.2%

Worsened metrics

Lines of code

4135

decreased by-0.22%

Dependency changes

• + Addedrxjs@7.8.2(transitive)

• + Addedtslib@2.8.1(transitive)

• - Removedrxjs@6.6.7(transitive)

• - Removedtslib@1.14.1(transitive)

• Updatedrxjs@^7.8.0