@jbrowse/plugin-bed 2.5.0 → 2.6.2

package/dist/BedAdapter/BedAdapter.js

@@ -86,7 +86,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return columnNames;
         }
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -132,4 +132,3 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedAdapter;
-//# sourceMappingURL=BedAdapter.js.map

package/dist/BedAdapter/configSchema.js

@@ -63,4 +63,3 @@ const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = BedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -39,7 +39,7 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         const header = await this.bed.getHeader();
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -71,4 +71,3 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedTabixAdapter;
-//# sourceMappingURL=BedTabixAdapter.js.map

package/dist/BedTabixAdapter/configSchema.js

@@ -60,4 +60,3 @@ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapte
     },
 }, { explicitlyTyped: true });
 exports.default = BedTabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedTabixAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -5,8 +5,8 @@ export declare function featureData(line: string, uniqueId: string, flip: boolea
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;
-        feats1: Record<string, string[]>;
-        feats2: Record<string, string[]>;
+        feats1: Record<string, string[] | undefined>;
+        feats2: Record<string, string[] | undefined>;
         columnNames: string[];
     }>;
     protected intervalTrees: {

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -91,7 +91,9 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             if (!feats2[r2]) {
                 feats2[r2] = [];
             }
+            // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
             feats1[r1].push(line);
+            // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
             feats2[r2].push(line);
         }
         const columnNames = this.getConf('columnNames');
@@ -125,7 +127,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return columnNames;
         }
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -147,11 +149,15 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const uniqueId = `${this.id}-${refName}-${i}`;
             return featureData(f, uniqueId, true, names);
         });
-        for (const obj of ret1) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        if (ret1) {
+            for (const obj of ret1) {
+                intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            }
         }
-        for (const obj of ret2) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        if (ret2) {
+            for (const obj of ret2) {
+                intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            }
         }
         return intervalTree;
     }
@@ -176,4 +182,3 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedpeAdapter;
-//# sourceMappingURL=BedpeAdapter.js.map

package/dist/BedpeAdapter/configSchema.js

@@ -28,4 +28,3 @@ const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = BedpeAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedpeAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedpeAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -11,15 +11,15 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const operators_1 = require("rxjs/operators");
-const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("../util");
 function isUCSC(f) {
     return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
 }
 class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre(opts) {
+        const pm = this.pluginManager;
         const bigbed = new bbi_1.BigBed({
-            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'bigBedLocation'), this.pluginManager),
+            filehandle: (0, io_1.openLocation)(this.getConf('bigBedLocation'), pm),
         });
         const header = await bigbed.getHeader(opts);
         const parser = new bed_1.default({ autoSql: header.autoSql });
@@ -107,4 +107,3 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources() { }
 }
 exports.default = BigBedAdapter;
-//# sourceMappingURL=BigBedAdapter.js.map

package/dist/BigBedAdapter/configSchema.js

@@ -15,4 +15,3 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
     },
 }, { explicitlyTyped: true });
 exports.default = BigBedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BigBedAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -84,7 +84,14 @@ class BedPlugin extends Plugin_1.default {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'BedpeAdapter') {
+                    return 'VariantTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
     }
 }
 exports.default = BedPlugin;
-//# sourceMappingURL=index.js.map

package/dist/util.js

@@ -104,11 +104,10 @@ function ucscProcessedTranscript(feature) {
     delete newData.blockCount;
     delete newData.thickStart;
     delete newData.thickEnd;
-    const newFeature = new util_1.SimpleFeature({
+    return new util_1.SimpleFeature({
         data: newData,
         id: feature.id(),
     });
-    return newFeature;
 }
 exports.ucscProcessedTranscript = ucscProcessedTranscript;
 function defaultParser(fields, line) {
@@ -156,4 +155,3 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
     return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
 }
 exports.featureData = featureData;
-//# sourceMappingURL=util.js.map

package/esm/BedAdapter/BedAdapter.js

@@ -81,7 +81,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
             return columnNames;
         }
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -127,4 +127,3 @@ class BedAdapter extends BaseFeatureDataAdapter {
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedAdapter;
-//# sourceMappingURL=BedAdapter.js.map

package/esm/BedAdapter/configSchema.js

@@ -61,4 +61,3 @@ const BedAdapter = ConfigurationSchema('BedAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -34,7 +34,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
         }
         const header = await this.bed.getHeader();
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -66,4 +66,3 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedTabixAdapter;
-//# sourceMappingURL=BedTabixAdapter.js.map

package/esm/BedTabixAdapter/configSchema.js

@@ -58,4 +58,3 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedTabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedTabixAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -5,8 +5,8 @@ export declare function featureData(line: string, uniqueId: string, flip: boolea
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;
-        feats1: Record<string, string[]>;
-        feats2: Record<string, string[]>;
+        feats1: Record<string, string[] | undefined>;
+        feats2: Record<string, string[] | undefined>;
         columnNames: string[];
     }>;
     protected intervalTrees: {

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -84,7 +84,9 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             if (!feats2[r2]) {
                 feats2[r2] = [];
             }
+            // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
             feats1[r1].push(line);
+            // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
             feats2[r2].push(line);
         }
         const columnNames = this.getConf('columnNames');
@@ -118,7 +120,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             return columnNames;
         }
         const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs[defs.length - 1];
+        const defline = defs.at(-1);
         return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
             ? defline
                 .slice(1)
@@ -140,11 +142,15 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             const uniqueId = `${this.id}-${refName}-${i}`;
             return featureData(f, uniqueId, true, names);
         });
-        for (const obj of ret1) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        if (ret1) {
+            for (const obj of ret1) {
+                intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            }
         }
-        for (const obj of ret2) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        if (ret2) {
+            for (const obj of ret2) {
+                intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            }
         }
         return intervalTree;
     }
@@ -169,4 +175,3 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedpeAdapter;
-//# sourceMappingURL=BedpeAdapter.js.map

package/esm/BedpeAdapter/configSchema.js

@@ -26,4 +26,3 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedpeAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedpeAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedpeAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -6,15 +6,15 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { map, mergeAll } from 'rxjs/operators';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { ucscProcessedTranscript } from '../util';
 function isUCSC(f) {
     return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
 }
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async configurePre(opts) {
+        const pm = this.pluginManager;
         const bigbed = new BigBed({
-            filehandle: openLocation(readConfObject(this.config, 'bigBedLocation'), this.pluginManager),
+            filehandle: openLocation(this.getConf('bigBedLocation'), pm),
         });
         const header = await bigbed.getHeader(opts);
         const parser = new BED({ autoSql: header.autoSql });
@@ -101,4 +101,3 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-//# sourceMappingURL=BigBedAdapter.js.map

package/esm/BigBedAdapter/configSchema.js

@@ -13,4 +13,3 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BigBedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BigBedAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -79,6 +79,13 @@ export default class BedPlugin extends Plugin {
                 return adapterGuesser(file, index, adapterHint);
             };
         });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'BedpeAdapter') {
+                    return 'VariantTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
     }
 }
-//# sourceMappingURL=index.js.map

package/esm/util.js

@@ -101,11 +101,10 @@ export function ucscProcessedTranscript(feature) {
     delete newData.blockCount;
     delete newData.thickStart;
     delete newData.thickEnd;
-    const newFeature = new SimpleFeature({
+    return new SimpleFeature({
         data: newData,
         id: feature.id(),
     });
-    return newFeature;
 }
 function defaultParser(fields, line) {
     return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
@@ -151,4 +150,3 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
     });
     return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.5.0",
+  "version": "2.6.2",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,12 +32,12 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^3.0.0",
+    "@gmod/bbi": "^4.0.0",
     "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.6"
@@ -56,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/BedAdapter/BedAdapter.js.map

@@ -1 +0,0 @@
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package/dist/BedpeAdapter/configSchema.js.map

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package/dist/BedpeAdapter/index.js.map

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package/dist/BigBedAdapter/BigBedAdapter.js.map

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package/dist/BigBedAdapter/index.js.map

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package/esm/BedAdapter/BedAdapter.js.map

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package/esm/BedAdapter/configSchema.js.map

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package/esm/BedAdapter/index.js.map

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package/esm/BedpeAdapter/configSchema.js.map

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