@jbrowse/plugin-gtf 3.6.4 → 3.7.0

package/dist/GtfAdapter/GtfAdapter.d.ts

@@ -1,15 +1,16 @@
-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 } from '@jbrowse/core/util';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 import type { Observer } from 'rxjs';
 type StatusCallback = (arg: string) => void;
+type SimpleFeat = SimpleFeatureSerialized;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    calculatedIntervalTreeMap: Record<string, IntervalTree<SimpleFeat>>;
     gtfFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<SimpleFeat>>;
     }>;
     private loadDataP;
     private loadData;

package/dist/GtfAdapter/GtfAdapter.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");
@@ -43,7 +40,7 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             (sc) => {
                 if (!this.calculatedIntervalTreeMap[refName]) {
                     sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
-                    const intervalTree = new interval_tree_1.default();
+                    const intervalTree = new interval_tree_1.IntervalTree();
                     for (const obj of (0, gtf_nostream_1.parseStringSync)(lines)
                         .flat()
                         .map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}`))) {
@@ -133,9 +130,6 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             }
             const parentAggregation = {};
-            if (feats.some(f => f.uniqueId === undefined)) {
-                throw new Error('found uniqueId undefined');
-            }
             for (const feat of feats) {
                 const aggr = feat[aggregateField];
                 if (!parentAggregation[aggr]) {

package/esm/GtfAdapter/GtfAdapter.d.ts

@@ -1,15 +1,16 @@
-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 } from '@jbrowse/core/util';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 import type { Observer } from 'rxjs';
 type StatusCallback = (arg: string) => void;
+type SimpleFeat = SimpleFeatureSerialized;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    calculatedIntervalTreeMap: Record<string, IntervalTree<SimpleFeat>>;
     gtfFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<SimpleFeat>>;
     }>;
     private loadDataP;
     private loadData;

package/esm/GtfAdapter/GtfAdapter.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, doesIntersect2, fetchAndMaybeUnzip, max, min, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -128,9 +128,6 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
                 }
             }
             const parentAggregation = {};
-            if (feats.some(f => f.uniqueId === undefined)) {
-                throw new Error('found uniqueId undefined');
-            }
             for (const feat of feats) {
                 const aggr = feat[aggregateField];
                 if (!parentAggregation[aggr]) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "3.6.4",
+  "version": "3.7.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -36,10 +36,10 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@flatten-js/interval-tree": "^1.0.15",
+    "@flatten-js/interval-tree": "^2.0.0",
     "@gmod/bgzf-filehandle": "^4.0.0",
-    "@jbrowse/core": "^3.6.4",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.4",
+    "@jbrowse/core": "^3.7.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
     "@mui/material": "^7.0.0",
     "gtf-nostream": "^1.0.0",
     "mobx": "^6.0.0",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }