@jbrowse/plugin-bed 5.0.0-beta.10 → 5.0.0-beta.11

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -14,9 +14,9 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
     // getFeatures/byte-estimate awaits it) doesn't re-flash "Downloading index"
     configure = cachedSetup({
         label: 'Downloading index',
-        setup: () => this.configurePre(),
+        setup: opts => this.configurePre(opts),
     });
-    async configurePre() {
+    async configurePre(opts) {
         const pm = this.pluginManager;
         const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
         const location = this.getConf(['index', 'location']);
@@ -31,7 +31,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
         // Not bedGraph.getHeader(): that returns only a `#`-commented header, so a
         // file whose header is a plain row skipped via `tabix -S 1` reported none
         // and quietly lost the names of its value columns.
-        const header = (await readTabixHeaderLines(bedGraph)).join('\n');
+        const header = (await readTabixHeaderLines(bedGraph, { signal: opts.signal })).join('\n');
         return {
             columnNames,
             bedGraph,

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -26,14 +26,14 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     // re-entry (every getFeatures awaits it) doesn't re-flash "Downloading index"
     getMetadata = cachedSetup({
         label: 'Downloading index',
-        setup: () => this.bed.getMetadata(),
+        setup: opts => this.bed.getMetadata({ signal: opts.signal }),
     });
     // Memoized: getFeatures needs the names on every query, and reading them goes
     // to the file's leading blocks — a fetch and a decompress that was being
     // repeated on every pan and zoom. Resolves undefined when the file declares
     // no column names — parseNamesFromHeader's answer for a header it can't read
     // names out of.
-    getNames = cachedSetup({ setup: () => this.readNames() });
+    getNames = cachedSetup({ setup: opts => this.readNames(opts.signal) });
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.bedGzLoc = readConfObject(this.config, 'bedGzLocation');
@@ -61,7 +61,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     async getRegionByteSize(regions, opts) {
         return this.bed.bytesForRegions(regions, opts);
     }
-    async readNames() {
+    async readNames(signal) {
         const columnNames = readConfObject(this.config, 'columnNames');
         if (columnNames.length) {
             return columnNames;
@@ -69,7 +69,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
         // readTabixHeaderLines covers both ways a tabix file keeps a header: a
         // `#`-commented block, which getHeader() returns, and a plain row skipped
         // via `tabix -S N`, which it does not.
-        return parseNamesFromHeader((await readTabixHeaderLines(this.bed)).join('\n'));
+        return parseNamesFromHeader((await readTabixHeaderLines(this.bed, { signal })).join('\n'));
     }
     getFeatures(query, opts) {
         const { signal, statusCallback } = opts ?? {};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.11",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -23,12 +23,16 @@
   "dependencies": {
     "@gmod/bbi": "^11.3.0",
     "@gmod/bed": "^2.3.1",
-    "@gmod/tabix": "^3.8.3",
+    "@gmod/tabix": "^3.9.1",
     "@gmod/trix": "^3.0.22",
-    "@jbrowse/mobx-state-tree": "^6.6.1",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
     "mobx": "^7.0.5",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.10"
+    "@jbrowse/core": "^5.0.0-beta.11"
+  },
+  "peerDependencies": {
+    "react": ">=19.0.0",
+    "react-dom": ">=19.0.0"
   },
   "publishConfig": {
     "access": "public"