@jbrowse/plugin-bed 3.1.0 → 3.2.0

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -119,9 +119,9 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureIntervalTree(refName);
-            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
-                observer.next(f);
-            });
+            for (const feature of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
+                observer.next(feature);
+            }
             observer.complete();
         });
     }

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -103,9 +103,9 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureTree(refName);
-            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+            for (const f of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
                 observer.next(f);
-            });
+            }
             observer.complete();
         }, opts.stopToken);
     }

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -9,7 +9,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: import("@gmod/bbi").Header;
+        header: import("@gmod/bbi/dist/types").BigWigHeaderWithRefNames;
         parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
@@ -18,6 +18,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getRefNameAliases(opts?: BaseOptions): Promise<{
+        refName: unknown;
+        aliases: unknown[];
+        override: boolean;
+    }[]>;
     getData(): Promise<Feature[]>;
     getHeader(opts?: BaseOptions): Promise<{
         version: number;

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -40,6 +40,22 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { header } = await this.configure(opts);
         return Object.keys(header.refsByName);
     }
+    async getRefNameAliases(opts) {
+        const { header } = await this.configure(opts);
+        const ret = await Promise.all(Object.keys(header.refsByName).map(async (r) => (await (0, rxjs_2.firstValueFrom)(this.getFeatures({
+            assemblyName: '',
+            refName: r,
+            start: 0,
+            end: 1,
+        }).pipe((0, rxjs_2.toArray)())))[0]));
+        return ret
+            .map(r => r.toJSON())
+            .map(r => ({
+            refName: r.ucsc,
+            aliases: [r.ncbi, r.refseq, r.genbank],
+            override: true,
+        }));
+    }
     async getData() {
         const refNames = await this.getRefNames();
         const features = [];
@@ -67,12 +83,11 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
         var _a;
-        const { stopToken, statusCallback = () => { } } = opts;
+        const { statusCallback = () => { } } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const { parser, bigbed } = await (0, util_1.updateStatus)('Downloading header', statusCallback, () => this.configure(opts));
         const feats = await (0, util_1.updateStatus)('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
-            stopToken,
             basesPerSpan: query.end - query.start,
         }));
         if (allowRedispatch && feats.length) {
@@ -95,8 +110,8 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 await this.getFeaturesHelper({
                     query: {
                         ...query,
-                        start: minStart,
-                        end: maxEnd,
+                        start: minStart - 500000,
+                        end: maxEnd + 500000,
                     },
                     opts,
                     observer,
@@ -148,16 +163,17 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
         }
         Object.entries(parentAggregation).map(([name, subfeatures]) => {
+            var _a, _b;
             const s = (0, util_1.min)(subfeatures.map(f => f.start));
             const e = (0, util_1.max)(subfeatures.map(f => f.end));
             if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
-                const { uniqueId, strand } = subfeatures[0];
+                const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
                 observer.next(new util_1.SimpleFeature({
-                    id: `${this.id}-${uniqueId}-parent`,
+                    id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
                     data: {
                         type: 'gene',
-                        subfeatures,
-                        strand,
+                        subfeatures: subs,
+                        strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
                         name,
                         start: s,
                         end: e,
@@ -172,7 +188,11 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             try {
                 await this.getFeaturesHelper({
-                    query,
+                    query: {
+                        ...query,
+                        start: query.start,
+                        end: query.end,
+                    },
                     opts,
                     observer,
                     allowRedispatch: true,

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -114,9 +114,9 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureIntervalTree(refName);
-            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
-                observer.next(f);
-            });
+            for (const feature of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
+                observer.next(feature);
+            }
             observer.complete();
         });
     }

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -98,9 +98,9 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureTree(refName);
-            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+            for (const f of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
                 observer.next(f);
-            });
+            }
             observer.complete();
         }, opts.stopToken);
     }

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -9,7 +9,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: import("@gmod/bbi").Header;
+        header: import("@gmod/bbi/dist/types").BigWigHeaderWithRefNames;
         parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
@@ -18,6 +18,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getRefNameAliases(opts?: BaseOptions): Promise<{
+        refName: unknown;
+        aliases: unknown[];
+        override: boolean;
+    }[]>;
     getData(): Promise<Feature[]>;
     getHeader(opts?: BaseOptions): Promise<{
         version: number;

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -35,6 +35,22 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         const { header } = await this.configure(opts);
         return Object.keys(header.refsByName);
     }
+    async getRefNameAliases(opts) {
+        const { header } = await this.configure(opts);
+        const ret = await Promise.all(Object.keys(header.refsByName).map(async (r) => (await firstValueFrom(this.getFeatures({
+            assemblyName: '',
+            refName: r,
+            start: 0,
+            end: 1,
+        }).pipe(toArray())))[0]));
+        return ret
+            .map(r => r.toJSON())
+            .map(r => ({
+            refName: r.ucsc,
+            aliases: [r.ncbi, r.refseq, r.genbank],
+            override: true,
+        }));
+    }
     async getData() {
         const refNames = await this.getRefNames();
         const features = [];
@@ -62,12 +78,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
         var _a;
-        const { stopToken, statusCallback = () => { } } = opts;
+        const { statusCallback = () => { } } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const { parser, bigbed } = await updateStatus('Downloading header', statusCallback, () => this.configure(opts));
         const feats = await updateStatus('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
-            stopToken,
             basesPerSpan: query.end - query.start,
         }));
         if (allowRedispatch && feats.length) {
@@ -90,8 +105,8 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 await this.getFeaturesHelper({
                     query: {
                         ...query,
-                        start: minStart,
-                        end: maxEnd,
+                        start: minStart - 500000,
+                        end: maxEnd + 500000,
                     },
                     opts,
                     observer,
@@ -143,16 +158,17 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             }
         }
         Object.entries(parentAggregation).map(([name, subfeatures]) => {
+            var _a, _b;
             const s = min(subfeatures.map(f => f.start));
             const e = max(subfeatures.map(f => f.end));
             if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
-                const { uniqueId, strand } = subfeatures[0];
+                const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
                 observer.next(new SimpleFeature({
-                    id: `${this.id}-${uniqueId}-parent`,
+                    id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
                     data: {
                         type: 'gene',
-                        subfeatures,
-                        strand,
+                        subfeatures: subs,
+                        strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
                         name,
                         start: s,
                         end: e,
@@ -167,7 +183,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             try {
                 await this.getFeaturesHelper({
-                    query,
+                    query: {
+                        ...query,
+                        start: query.start,
+                        end: query.end,
+                    },
                     opts,
                     observer,
                     allowRedispatch: true,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "3.1.0",
+  "version": "3.2.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -41,7 +41,7 @@
     "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/tabix": "^2.0.0",
-    "@jbrowse/core": "^3.1.0",
+    "@jbrowse/core": "^3.2.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -53,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }