@jbrowse/plugin-bed 3.1.0 → 3.3.0

package/dist/BedAdapter/configSchema.d.ts

@@ -1,6 +1,7 @@
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     bedLocation: {
         type: string;
+        description: string;
         defaultValue: {
             uri: string;
             locationType: string;

package/dist/BedAdapter/configSchema.js

@@ -5,6 +5,7 @@ function x() { }
 const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
     bedLocation: {
         type: 'fileLocation',
+        description: 'path to bed file, also allows gzipped bed',
         defaultValue: {
             uri: '/path/to/my.bed.gz',
             locationType: 'UriLocation',

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/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -40,5 +40,4 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     }>;
     getNames(): Promise<string[] | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -99,7 +99,6 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, stopToken);
     }
-    freeResources() { }
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedTabixAdapter;

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/BedpeAdapter/configSchema.d.ts

@@ -1,6 +1,7 @@
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     bedpeLocation: {
         type: string;
+        description: string;
         defaultValue: {
             uri: string;
             locationType: string;

package/dist/BedpeAdapter/configSchema.js

@@ -5,6 +5,7 @@ function x() { }
 const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
     bedpeLocation: {
         type: 'fileLocation',
+        description: 'can be plaintext or gzipped, not indexed so loaded into memory on startup',
         defaultValue: {
             uri: '/path/to/my.bedpe.gz',
             locationType: 'UriLocation',

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 = [];
@@ -67,46 +83,15 @@ 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) {
-            let minStart = Number.POSITIVE_INFINITY;
-            let maxEnd = Number.NEGATIVE_INFINITY;
-            let hasAnyAggregationField = false;
-            for (const feat of feats) {
-                if (feat.start < minStart) {
-                    minStart = feat.start;
-                }
-                if (feat.end > maxEnd) {
-                    maxEnd = feat.end;
-                }
-                if (feat[aggregateField]) {
-                    hasAnyAggregationField = true;
-                }
-            }
-            if (hasAnyAggregationField &&
-                (maxEnd > query.end || minStart < query.start)) {
-                await this.getFeaturesHelper({
-                    query: {
-                        ...query,
-                        start: minStart,
-                        end: maxEnd,
-                    },
-                    opts,
-                    observer,
-                    allowRedispatch: false,
-                    originalQuery: query,
-                });
-                return;
-            }
-        }
         const parentAggregation = {};
+        const parentAggregationFlat = [];
         if (feats.some(f => f.uniqueId === undefined)) {
             throw new Error('found uniqueId undefined');
         }
@@ -137,6 +122,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             });
             if (aggr) {
                 parentAggregation[aggr].push(f);
+                parentAggregationFlat.push(f);
             }
             else {
                 if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
@@ -147,17 +133,44 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             }
         }
+        if (allowRedispatch && parentAggregationFlat.length) {
+            let minStart = Number.POSITIVE_INFINITY;
+            let maxEnd = Number.NEGATIVE_INFINITY;
+            for (const feat of parentAggregationFlat) {
+                if (feat.start < minStart) {
+                    minStart = feat.start;
+                }
+                if (feat.end > maxEnd) {
+                    maxEnd = feat.end;
+                }
+            }
+            if (maxEnd > query.end || minStart < query.start) {
+                await this.getFeaturesHelper({
+                    query: {
+                        ...query,
+                        start: minStart - 500000,
+                        end: maxEnd + 500000,
+                    },
+                    opts,
+                    observer,
+                    allowRedispatch: false,
+                    originalQuery: query,
+                });
+                return;
+            }
+        }
         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 +185,11 @@ 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/BedAdapter/configSchema.d.ts

@@ -1,6 +1,7 @@
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     bedLocation: {
         type: string;
+        description: string;
         defaultValue: {
             uri: string;
             locationType: string;

package/esm/BedAdapter/configSchema.js

@@ -3,6 +3,7 @@ function x() { }
 const BedAdapter = ConfigurationSchema('BedAdapter', {
     bedLocation: {
         type: 'fileLocation',
+        description: 'path to bed file, also allows gzipped bed',
         defaultValue: {
             uri: '/path/to/my.bed.gz',
             locationType: 'UriLocation',

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/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -40,5 +40,4 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     }>;
     getNames(): Promise<string[] | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -94,7 +94,6 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, stopToken);
     }
-    freeResources() { }
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedTabixAdapter;

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/BedpeAdapter/configSchema.d.ts

@@ -1,6 +1,7 @@
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     bedpeLocation: {
         type: string;
+        description: string;
         defaultValue: {
             uri: string;
             locationType: string;

package/esm/BedpeAdapter/configSchema.js

@@ -3,6 +3,7 @@ function x() { }
 const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
     bedpeLocation: {
         type: 'fileLocation',
+        description: 'can be plaintext or gzipped, not indexed so loaded into memory on startup',
         defaultValue: {
             uri: '/path/to/my.bedpe.gz',
             locationType: 'UriLocation',

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 = [];
@@ -62,46 +78,15 @@ 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) {
-            let minStart = Number.POSITIVE_INFINITY;
-            let maxEnd = Number.NEGATIVE_INFINITY;
-            let hasAnyAggregationField = false;
-            for (const feat of feats) {
-                if (feat.start < minStart) {
-                    minStart = feat.start;
-                }
-                if (feat.end > maxEnd) {
-                    maxEnd = feat.end;
-                }
-                if (feat[aggregateField]) {
-                    hasAnyAggregationField = true;
-                }
-            }
-            if (hasAnyAggregationField &&
-                (maxEnd > query.end || minStart < query.start)) {
-                await this.getFeaturesHelper({
-                    query: {
-                        ...query,
-                        start: minStart,
-                        end: maxEnd,
-                    },
-                    opts,
-                    observer,
-                    allowRedispatch: false,
-                    originalQuery: query,
-                });
-                return;
-            }
-        }
         const parentAggregation = {};
+        const parentAggregationFlat = [];
         if (feats.some(f => f.uniqueId === undefined)) {
             throw new Error('found uniqueId undefined');
         }
@@ -132,6 +117,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             });
             if (aggr) {
                 parentAggregation[aggr].push(f);
+                parentAggregationFlat.push(f);
             }
             else {
                 if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
@@ -142,17 +128,44 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 }
             }
         }
+        if (allowRedispatch && parentAggregationFlat.length) {
+            let minStart = Number.POSITIVE_INFINITY;
+            let maxEnd = Number.NEGATIVE_INFINITY;
+            for (const feat of parentAggregationFlat) {
+                if (feat.start < minStart) {
+                    minStart = feat.start;
+                }
+                if (feat.end > maxEnd) {
+                    maxEnd = feat.end;
+                }
+            }
+            if (maxEnd > query.end || minStart < query.start) {
+                await this.getFeaturesHelper({
+                    query: {
+                        ...query,
+                        start: minStart - 500000,
+                        end: maxEnd + 500000,
+                    },
+                    opts,
+                    observer,
+                    allowRedispatch: false,
+                    originalQuery: query,
+                });
+                return;
+            }
+        }
         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 +180,11 @@ 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": "3.3.0",
   "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": "^3.3.0",
     "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": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }