@jbrowse/plugin-variants 2.16.1 → 2.17.0

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/VcfAdapter/VcfAdapter.js

@@ -8,7 +8,6 @@ const util_1 = require("@jbrowse/core/util");
 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 bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
@@ -28,20 +27,18 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await (0, io_1.openLocation)(this.getConf('vcfLocation'), 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('vcfLocation'), this.pluginManager);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         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/VariantFeatureWidget/stateModelFactory.d.ts

@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,9 +1,8 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { updateStatus, isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
-import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
 // local
 import VcfFeature from '../VcfFeature';
@@ -23,20 +22,18 @@ class VcfAdapter extends BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const loc = openLocation(this.getConf('vcfLocation'), this.pluginManager);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         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-variants",
-  "version": "2.16.1",
+  "version": "2.17.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -40,7 +40,7 @@
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
-    "@jbrowse/sv-core": "^2.16.1",
+    "@jbrowse/sv-core": "^2.17.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "generic-filehandle": "^3.0.0"
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }