@jbrowse/plugin-gtf 2.16.0 → 2.17.0

package/dist/GtfAdapter/GtfAdapter.js

@@ -8,11 +8,9 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const util_1 = require("@jbrowse/core/util");
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const gtf_nostream_1 = require("gtf-nostream");
 // locals
 const util_2 = require("../util");
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -20,19 +18,18 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await (0, io_1.openLocation)(this.getConf('gtfLocation'), this.pluginManager).readFile(opts));
-        const buffer = (0, util_1.isGzip)(buf)
-            ? await (0, util_1.updateStatus)('Unzipping', statusCallback, () => (0, bgzf_filehandle_1.unzip)(buf))
-            : buf;
+        const loc = (0, io_1.openLocation)(this.getConf('gtfLocation'), this.pluginManager);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
         let i = 0;
+        const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
             // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);

package/esm/GtfAdapter/GtfAdapter.js

@@ -2,12 +2,10 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
-import { SimpleFeature, updateStatus, isGzip, } from '@jbrowse/core/util';
-import { unzip } from '@gmod/bgzf-filehandle';
+import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { parseStringSync } from 'gtf-nostream';
 // locals
 import { featureData } from '../util';
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -15,19 +13,18 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('gtfLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const loc = openLocation(this.getConf('gtfLocation'), this.pluginManager);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
         let i = 0;
+        const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
             // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }