@jbrowse/plugin-gff3 1.7.10 → 1.7.11

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -29,8 +29,6 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
 
-var _configuration = require("@jbrowse/core/configuration");
-
 var _io = require("@jbrowse/core/util/io");
 
 var _rxjs = require("@jbrowse/core/util/rxjs");
@@ -80,47 +78,48 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var _this2 = this;
 
-        var buffer, buf, data, lines, headerLines, i, header, feats, intervalTree;
+        var pm, buf, buffer, data, lines, headerLines, i, header, feats, intervalTree;
         return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                _context.next = 2;
-                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'gffLocation'), this.pluginManager).readFile();
+                pm = this.pluginManager;
+                _context.next = 3;
+                return (0, _io.openLocation)(this.getConf('gffLocation'), pm).readFile();
 
-              case 2:
-                buffer = _context.sent;
+              case 3:
+                buf = _context.sent;
 
-                if (!isGzip(buffer)) {
-                  _context.next = 9;
+                if (!isGzip(buf)) {
+                  _context.next = 10;
                   break;
                 }
 
-                _context.next = 6;
-                return (0, _bgzfFilehandle.unzip)(buffer);
+                _context.next = 7;
+                return (0, _bgzfFilehandle.unzip)(buf);
 
-              case 6:
+              case 7:
                 _context.t0 = _context.sent;
-                _context.next = 10;
+                _context.next = 11;
                 break;
 
-              case 9:
-                _context.t0 = buffer;
-
               case 10:
-                buf = _context.t0;
+                _context.t0 = buf;
+
+              case 11:
+                buffer = _context.t0;
 
-                if (!(buf.length > 536870888)) {
-                  _context.next = 13;
+                if (!(buffer.length > 536870888)) {
+                  _context.next = 14;
                   break;
                 }
 
                 throw new Error('Data exceeds maximum string length (512MB)');
 
-              case 13:
+              case 14:
                 data = new TextDecoder('utf8', {
                   fatal: true
-                }).decode(buf);
+                }).decode(buffer);
                 lines = data.split('\n');
                 headerLines = [];
 
@@ -155,7 +154,7 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   intervalTree: intervalTree
                 });
 
-              case 21:
+              case 22:
               case "end":
                 return _context.stop();
             }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.7.10",
+  "version": "1.7.11",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -52,5 +52,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
+  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
 }

package/src/Gff3Adapter/Gff3Adapter.ts

@@ -3,7 +3,6 @@ import {
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import IntervalTree from '@flatten-js/interval-tree'
@@ -23,16 +22,14 @@ export default class extends BaseFeatureDataAdapter {
   }>
 
   private async loadDataP() {
-    const buffer = await openLocation(
-      readConfObject(this.config, 'gffLocation'),
-      this.pluginManager,
-    ).readFile()
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
+    const pm = this.pluginManager
+    const buf = await openLocation(this.getConf('gffLocation'), pm).readFile()
+    const buffer = isGzip(buf) ? await unzip(buf) : buf
     // 512MB  max chrome string length is 512MB
-    if (buf.length > 536_870_888) {
+    if (buffer.length > 536_870_888) {
       throw new Error('Data exceeds maximum string length (512MB)')
     }
-    const data = new TextDecoder('utf8', { fatal: true }).decode(buf)
+    const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)
     const lines = data.split('\n')
     const headerLines = []
     for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {