@jbrowse/plugin-bed 3.6.4 → 3.7.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -14,7 +14,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
         colStart: number;
         colEnd: number;
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     loadData(opts?: BaseOptions): Promise<{
@@ -31,6 +31,6 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/dist/BedAdapter/BedAdapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const interval_tree_1 = require("@flatten-js/interval-tree");
 const bed_1 = __importDefault(require("@gmod/bed"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
@@ -92,7 +92,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return undefined;
         }
         const names = await this.getNames();
-        const intervalTree = new interval_tree_1.default();
+        const intervalTree = new interval_tree_1.IntervalTree();
         for (let i = 0; i < lines.length; i++) {
             const line = lines[i];
             const uniqueId = `${this.id}-${refName}-${i}`;

package/dist/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -8,12 +8,12 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         features: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private loadDataP;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     loadData(opts?: BaseOptions): Promise<{
         header: string;
         features: Record<string, string[]>;

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -1,9 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const interval_tree_1 = require("@flatten-js/interval-tree");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
@@ -36,11 +33,11 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return undefined;
         }
         const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(3)) || [];
-        const intervalTree = new interval_tree_1.default();
-        for (let i = 0; i < lines.length; i++) {
+        const intervalTree = new interval_tree_1.IntervalTree();
+        for (let i = 0, l = lines.length; i < l; i++) {
             const line = lines[i];
             const [refName, s, e, ...rest] = line.split('\t');
-            for (let j = 0; j < rest.length; j++) {
+            for (let j = 0, l2 = rest.length; j < l2; j++) {
                 const uniqueId = `${this.id}-${refName}-${i}-${j}`;
                 const start = +s;
                 const end = +e;

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -25,7 +25,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             [key: string]: any;
             refNameToId: Record<string, number>;
             refIdToName: string[];
-            metaChar: string | null;
+            metaChar: string | undefined;
             columnNumbers: {
                 ref: number;
                 start: number;

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -9,7 +9,7 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
         feats2: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     private loadData;

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -1,9 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const interval_tree_1 = require("@flatten-js/interval-tree");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
@@ -82,7 +79,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         var _a, _b, _c, _d;
         const { feats1, feats2 } = await this.loadData();
         const names = await this.getNames();
-        const intervalTree = new interval_tree_1.default();
+        const intervalTree = new interval_tree_1.IntervalTree();
         const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
         const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
         for (const obj of [...ret1, ...ret2]) {

package/esm/BedAdapter/BedAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -14,7 +14,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
         colStart: number;
         colEnd: number;
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     loadData(opts?: BaseOptions): Promise<{
@@ -31,6 +31,6 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+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';

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -8,12 +8,12 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         features: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private loadDataP;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     loadData(opts?: BaseOptions): Promise<{
         header: string;
         features: Record<string, string[]>;

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -32,10 +32,10 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         }
         const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(3)) || [];
         const intervalTree = new IntervalTree();
-        for (let i = 0; i < lines.length; i++) {
+        for (let i = 0, l = lines.length; i < l; i++) {
             const line = lines[i];
             const [refName, s, e, ...rest] = line.split('\t');
-            for (let j = 0; j < rest.length; j++) {
+            for (let j = 0, l2 = rest.length; j < l2; j++) {
                 const uniqueId = `${this.id}-${refName}-${i}-${j}`;
                 const start = +s;
                 const end = +e;

package/esm/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -25,7 +25,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             [key: string]: any;
             refNameToId: Record<string, number>;
             refIdToName: string[];
-            metaChar: string | null;
+            metaChar: string | undefined;
             columnNumbers: {
                 ref: number;
                 start: number;

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -9,7 +9,7 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
         feats2: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     private loadData;

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "3.6.4",
+  "version": "3.7.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,12 +36,12 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@flatten-js/interval-tree": "^1.0.15",
+    "@flatten-js/interval-tree": "^2.0.0",
     "@gmod/bbi": "^7.0.0",
     "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^4.0.0",
     "@gmod/tabix": "^3.0.1",
-    "@jbrowse/core": "^3.6.4",
+    "@jbrowse/core": "^3.7.0",
     "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": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }