@jbrowse/plugin-bed 3.3.0 → 3.4.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -33,5 +33,4 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     private loadFeatureIntervalTreeHelper;
     loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedAdapter/BedAdapter.js

@@ -15,31 +15,41 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
-        const pm = this.pluginManager;
+    async loadDataP(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const bedLoc = this.getConf('bedLocation');
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
-        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, this.pluginManager), opts);
         const headerLines = [];
-        let i = 0;
-        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-            headerLines.push(lines[i]);
-        }
-        const header = headerLines.join('\n');
         const features = {};
-        for (; i < lines.length; i++) {
-            const line = lines[i];
-            const tab = line.indexOf('\t');
-            const refName = line.slice(0, tab);
-            if (!features[refName]) {
-                features[refName] = [];
+        let blockStart = 0;
+        let i = 0;
+        const decoder = new TextDecoder('utf8');
+        while (blockStart < buffer.length) {
+            const n = buffer.indexOf(10, blockStart);
+            const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
+            const line = decoder.decode(b).trim();
+            if (line) {
+                if (line.startsWith('#')) {
+                    headerLines.push(line);
+                }
+                else if (line.startsWith('>')) {
+                    break;
+                }
+                else {
+                    const tab = line.indexOf('\t');
+                    const refName = line.slice(0, tab);
+                    if (!features[refName]) {
+                        features[refName] = [];
+                    }
+                    features[refName].push(line);
+                }
             }
-            features[refName].push(line);
+            if (i++ % 10000 === 0) {
+                statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
+            }
+            blockStart = n + 1;
         }
+        const header = headerLines.join('\n');
         const autoSql = this.getConf('autoSql');
         const parser = new bed_1.default({ autoSql });
         const columnNames = this.getConf('columnNames');
@@ -136,7 +146,6 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedAdapter;

package/dist/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -20,5 +20,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         columnNames: string[];
     }>;
     getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -125,6 +125,5 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 exports.default = BedGraphAdapter;

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -14,5 +14,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(): Promise<string>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -103,6 +103,5 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 exports.default = BedGraphAdapter;

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -19,5 +19,4 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
     private loadFeatureTreeP;
     private loadFeatureTree;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -109,7 +109,6 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedpeAdapter;

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -32,6 +32,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
+    getMetadata(opts?: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
     getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
         query: Region;
         opts: BaseOptions;
@@ -40,5 +43,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         originalQuery?: Region;
     }): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -78,9 +78,14 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             version,
             fileType,
             autoSql: { ...rest },
-            fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
+            fields: await this.getMetadata(opts),
         };
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        const { fields } = parser.autoSql;
+        return Object.fromEntries(fields.map(({ name, comment }) => [name, comment]));
+    }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
         var _a;
         const { statusCallback = () => { } } = opts;
@@ -106,7 +111,8 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 uniqueId: feat.uniqueId,
             });
             const aggr = data[aggregateField];
-            if (!parentAggregation[aggr]) {
+            const aggrIsNotNone = aggr && aggr !== 'none';
+            if (aggrIsNotNone && !parentAggregation[aggr]) {
                 parentAggregation[aggr] = [];
             }
             const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
@@ -120,7 +126,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 end: feat.end,
                 refName: query.refName,
             });
-            if (aggr) {
+            if (aggrIsNotNone) {
                 parentAggregation[aggr].push(f);
                 parentAggregationFlat.push(f);
             }
@@ -200,6 +206,5 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 exports.default = BigBedAdapter;

package/esm/BedAdapter/BedAdapter.d.ts

@@ -33,5 +33,4 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     private loadFeatureIntervalTreeHelper;
     loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -1,7 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { SimpleFeature, fetchAndMaybeUnzip, getProgressDisplayStr, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { featureData } from '../util';
@@ -10,31 +10,41 @@ class BedAdapter extends BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
-        const pm = this.pluginManager;
+    async loadDataP(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const bedLoc = this.getConf('bedLocation');
-        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
-        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, this.pluginManager), opts);
         const headerLines = [];
-        let i = 0;
-        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-            headerLines.push(lines[i]);
-        }
-        const header = headerLines.join('\n');
         const features = {};
-        for (; i < lines.length; i++) {
-            const line = lines[i];
-            const tab = line.indexOf('\t');
-            const refName = line.slice(0, tab);
-            if (!features[refName]) {
-                features[refName] = [];
+        let blockStart = 0;
+        let i = 0;
+        const decoder = new TextDecoder('utf8');
+        while (blockStart < buffer.length) {
+            const n = buffer.indexOf(10, blockStart);
+            const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
+            const line = decoder.decode(b).trim();
+            if (line) {
+                if (line.startsWith('#')) {
+                    headerLines.push(line);
+                }
+                else if (line.startsWith('>')) {
+                    break;
+                }
+                else {
+                    const tab = line.indexOf('\t');
+                    const refName = line.slice(0, tab);
+                    if (!features[refName]) {
+                        features[refName] = [];
+                    }
+                    features[refName].push(line);
+                }
             }
-            features[refName].push(line);
+            if (i++ % 10000 === 0) {
+                statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
+            }
+            blockStart = n + 1;
         }
+        const header = headerLines.join('\n');
         const autoSql = this.getConf('autoSql');
         const parser = new BED({ autoSql });
         const columnNames = this.getConf('columnNames');
@@ -131,7 +141,6 @@ class BedAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedAdapter;

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -20,5 +20,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         columnNames: string[];
     }>;
     getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -120,5 +120,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -14,5 +14,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(): Promise<string>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -101,5 +101,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -19,5 +19,4 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
     private loadFeatureTreeP;
     private loadFeatureTree;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -104,7 +104,6 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedpeAdapter;

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -32,6 +32,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
+    getMetadata(opts?: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
     getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
         query: Region;
         opts: BaseOptions;
@@ -40,5 +43,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         originalQuery?: Region;
     }): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -73,9 +73,14 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             version,
             fileType,
             autoSql: { ...rest },
-            fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
+            fields: await this.getMetadata(opts),
         };
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        const { fields } = parser.autoSql;
+        return Object.fromEntries(fields.map(({ name, comment }) => [name, comment]));
+    }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
         var _a;
         const { statusCallback = () => { } } = opts;
@@ -101,7 +106,8 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 uniqueId: feat.uniqueId,
             });
             const aggr = data[aggregateField];
-            if (!parentAggregation[aggr]) {
+            const aggrIsNotNone = aggr && aggr !== 'none';
+            if (aggrIsNotNone && !parentAggregation[aggr]) {
                 parentAggregation[aggr] = [];
             }
             const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
@@ -115,7 +121,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 end: feat.end,
                 refName: query.refName,
             });
-            if (aggr) {
+            if (aggrIsNotNone) {
                 parentAggregation[aggr].push(f);
                 parentAggregationFlat.push(f);
             }
@@ -195,5 +201,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
-    freeResources() { }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "3.3.0",
+  "version": "3.4.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,11 +37,11 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^6.0.0",
+    "@gmod/bbi": "^7.0.0",
     "@gmod/bed": "^2.1.2",
-    "@gmod/bgzf-filehandle": "^2.0.1",
-    "@gmod/tabix": "^2.0.0",
-    "@jbrowse/core": "^3.3.0",
+    "@gmod/bgzf-filehandle": "^3.0.2",
+    "@gmod/tabix": "^3.0.1",
+    "@jbrowse/core": "^3.4.0",
     "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": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
 }