@jbrowse/plugin-bed 2.13.0 → 2.14.0

package/dist/BedAdapter/BedAdapter.js

@@ -7,13 +7,11 @@ const bed_1 = __importDefault(require("@gmod/bed"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const util_1 = require("@jbrowse/core/util");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 // locals
-const util_1 = require("../util");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+const util_2 = require("../util");
 class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -23,7 +21,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedLocation');
         const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
-        const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        const buffer = (0, util_1.isGzip)(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
@@ -66,7 +64,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadData(opts = {}) {
         if (!this.bedFeatures) {
-            this.bedFeatures = this.loadDataP(opts).catch(e => {
+            this.bedFeatures = this.loadDataP(opts).catch((e) => {
                 this.bedFeatures = undefined;
                 throw e;
             });
@@ -105,7 +103,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const intervalTree = new interval_tree_1.default();
         const ret = lines.map((f, i) => {
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return (0, util_1.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+            return (0, util_2.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
         });
         for (const obj of ret) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);
@@ -114,7 +112,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadFeatureIntervalTree(refName) {
         if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(e => {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
                 this.intervalTrees[refName] = undefined;
                 throw e;
             });
@@ -125,7 +123,9 @@ class BedAdapter 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));
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+                observer.next(f);
+            });
             observer.complete();
         }, opts.signal);
     }

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[] | undefined>;
-        feats2: Record<string, string[] | undefined>;
+        feats1: Record<string, string[]>;
+        feats2: Record<string, string[]>;
         columnNames: string[];
     }>;
     protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -10,9 +10,6 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
     const ref1 = l[flip ? 3 : 0];
@@ -29,10 +26,9 @@ function featureData(line, uniqueId, flip, names) {
     const rest = names
         ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
         : extra;
-    let ALT;
-    if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])) {
-        ALT = `<${extra[0]}>`;
-    }
+    const ALT = ['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])
+        ? `<${extra[0]}>`
+        : undefined;
     return new util_1.SimpleFeature({
         start: start1,
         end: end1,
@@ -50,15 +46,13 @@ function parseStrand(strand) {
     if (strand === '+') {
         return 1;
     }
-    else if (strand === '-') {
+    if (strand === '-') {
         return -1;
     }
-    else if (strand === '.') {
+    if (strand === '.') {
         return 0;
     }
-    else {
-        return undefined;
-    }
+    return undefined;
 }
 class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -69,7 +63,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedpeLocation');
         const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
-        const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        const buffer = (0, util_1.isGzip)(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
@@ -108,7 +102,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadData(opts = {}) {
         if (!this.bedpeFeatures) {
-            this.bedpeFeatures = this.loadDataP(opts).catch(e => {
+            this.bedpeFeatures = this.loadDataP(opts).catch((e) => {
                 this.bedpeFeatures = undefined;
                 throw e;
             });
@@ -151,7 +145,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadFeatureTree(refName) {
         if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(e => {
+            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch((e) => {
                 this.intervalTrees[refName] = undefined;
                 throw e;
             });
@@ -162,7 +156,9 @@ 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 => observer.next(f));
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+                observer.next(f);
+            });
             observer.complete();
         }, opts.signal);
     }

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -25,7 +25,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
-    getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeaturesHelper(query: Region, opts: BaseOptions, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -23,7 +23,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async configure(opts) {
         if (!this.cached) {
-            this.cached = this.configurePre(opts).catch(e => {
+            this.cached = this.configurePre(opts).catch((e) => {
                 this.cached = undefined;
                 throw e;
             });
@@ -45,7 +45,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
+    async getFeaturesHelper(query, opts, observer, allowRedispatch, originalQuery = query) {
         const { signal } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
@@ -55,8 +55,8 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             basesPerSpan: query.end - query.start,
         });
         if (allowRedispatch && feats.length) {
-            let minStart = Infinity;
-            let maxEnd = -Infinity;
+            let minStart = Number.POSITIVE_INFINITY;
+            let maxEnd = Number.NEGATIVE_INFINITY;
             for (const feat of feats) {
                 if (feat.start < minStart) {
                     minStart = feat.start;

package/dist/index.js

@@ -31,7 +31,7 @@ class BedPlugin extends Plugin_1.default {
                 if (regexGuess.test(fileName) && !adapterHint) {
                     return obj;
                 }
-                else if (adapterHint === adapterName) {
+                if (adapterHint === adapterName) {
                     return obj;
                 }
                 return adapterGuesser(file, index, adapterHint);

package/dist/util.d.ts

@@ -30,9 +30,9 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     start: number;
     uniqueId: string;
     refName: string;
-    chromStarts: number[];
+    chromStarts?: number[];
     blockSizes: number[];
-    blockStarts: number[];
+    blockStarts?: number[];
 }): {
     uniqueId: string;
     start: number;

package/dist/util.js

@@ -6,15 +6,15 @@ exports.featureData = featureData;
 exports.isUcscProcessedTranscript = isUcscProcessedTranscript;
 const util_1 = require("@jbrowse/core/util");
 function ucscProcessedTranscript(feature) {
-    var _a;
     const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
     if (!thickStart || !thickEnd || !strand) {
         return feature;
     }
     const subfeatures = [];
-    (_a = oldSubfeatures
+    oldSubfeatures
         .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start)) === null || _a === void 0 ? void 0 : _a.forEach(block => {
+        .sort((a, b) => a.start - b.start)
+        .forEach(block => {
         const start = block.start;
         const end = block.end;
         if (thickStart >= end) {
@@ -61,7 +61,7 @@ function ucscProcessedTranscript(feature) {
                 end: thickStart,
                 refName,
             }, {
-                type: `CDS`,
+                type: 'CDS',
                 start: thickStart,
                 end: thickEnd,
                 refName,
@@ -76,7 +76,7 @@ function ucscProcessedTranscript(feature) {
             // CDS | UTR
             const prime = strand > 0 ? 'three' : 'five';
             subfeatures.push({
-                type: `CDS`,
+                type: 'CDS',
                 start,
                 end: thickEnd,
                 refName,
@@ -101,15 +101,16 @@ function ucscProcessedTranscript(feature) {
     return { ...rest, strand, type: 'mRNA', refName, subfeatures };
 }
 function defaultParser(fields, line) {
-    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
+    const obj = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
+    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
     return {
         ...rest,
         blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
         chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
         blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
-        thickStart: +thickStart,
-        thickEnd: +thickEnd,
-        blockCount: +blockCount,
+        thickStart: thickStart ? +thickStart : undefined,
+        thickEnd: thickEnd ? +thickEnd : undefined,
+        blockCount: blockCount ? +blockCount : undefined,
     };
 }
 function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
@@ -117,7 +118,7 @@ function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSi
     const starts = chromStarts || blockStarts || [];
     for (let b = 0; b < blockCount; b++) {
         const bmin = (starts[b] || 0) + start;
-        const bmax = bmin + ((blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b]) || 0);
+        const bmax = bmin + (blockSizes[b] || 0);
         subfeatures.push({
             uniqueId: `${uniqueId}-${b}`,
             start: bmin,
@@ -163,11 +164,11 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
         id: uniqueId,
         data: isUcscProcessedTranscript(data)
             ? ucscProcessedTranscript({
-                thickStart,
-                thickEnd,
-                blockCount,
-                blockSizes,
-                chromStarts,
+                thickStart: thickStart,
+                thickEnd: thickEnd,
+                blockCount: blockCount,
+                blockSizes: blockSizes,
+                chromStarts: chromStarts,
                 ...f,
             })
             : f,

package/esm/BedAdapter/BedAdapter.js

@@ -2,13 +2,11 @@ import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { isGzip } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
 import { unzip } from '@gmod/bgzf-filehandle';
 // locals
 import { featureData } from '../util';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 class BedAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -61,7 +59,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
     }
     async loadData(opts = {}) {
         if (!this.bedFeatures) {
-            this.bedFeatures = this.loadDataP(opts).catch(e => {
+            this.bedFeatures = this.loadDataP(opts).catch((e) => {
                 this.bedFeatures = undefined;
                 throw e;
             });
@@ -109,7 +107,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
     }
     async loadFeatureIntervalTree(refName) {
         if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(e => {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
                 this.intervalTrees[refName] = undefined;
                 throw e;
             });
@@ -120,7 +118,9 @@ class BedAdapter 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));
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+                observer.next(f);
+            });
             observer.complete();
         }, opts.signal);
     }

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[] | undefined>;
-        feats2: Record<string, string[] | undefined>;
+        feats1: Record<string, string[]>;
+        feats2: Record<string, string[]>;
         columnNames: string[];
     }>;
     protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,12 +1,9 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
+import { SimpleFeature, isGzip } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
 import { unzip } from '@gmod/bgzf-filehandle';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 export function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
     const ref1 = l[flip ? 3 : 0];
@@ -23,10 +20,9 @@ export function featureData(line, uniqueId, flip, names) {
     const rest = names
         ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
         : extra;
-    let ALT;
-    if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])) {
-        ALT = `<${extra[0]}>`;
-    }
+    const ALT = ['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])
+        ? `<${extra[0]}>`
+        : undefined;
     return new SimpleFeature({
         start: start1,
         end: end1,
@@ -44,15 +40,13 @@ function parseStrand(strand) {
     if (strand === '+') {
         return 1;
     }
-    else if (strand === '-') {
+    if (strand === '-') {
         return -1;
     }
-    else if (strand === '.') {
+    if (strand === '.') {
         return 0;
     }
-    else {
-        return undefined;
-    }
+    return undefined;
 }
 class BedpeAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -102,7 +96,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
     }
     async loadData(opts = {}) {
         if (!this.bedpeFeatures) {
-            this.bedpeFeatures = this.loadDataP(opts).catch(e => {
+            this.bedpeFeatures = this.loadDataP(opts).catch((e) => {
                 this.bedpeFeatures = undefined;
                 throw e;
             });
@@ -145,7 +139,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
     }
     async loadFeatureTree(refName) {
         if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(e => {
+            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch((e) => {
                 this.intervalTrees[refName] = undefined;
                 throw e;
             });
@@ -156,7 +150,9 @@ 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 => observer.next(f));
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+                observer.next(f);
+            });
             observer.complete();
         }, opts.signal);
     }

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -25,7 +25,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
-    getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeaturesHelper(query: Region, opts: BaseOptions, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -18,7 +18,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     async configure(opts) {
         if (!this.cached) {
-            this.cached = this.configurePre(opts).catch(e => {
+            this.cached = this.configurePre(opts).catch((e) => {
                 this.cached = undefined;
                 throw e;
             });
@@ -40,7 +40,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
+    async getFeaturesHelper(query, opts, observer, allowRedispatch, originalQuery = query) {
         const { signal } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
@@ -50,8 +50,8 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             basesPerSpan: query.end - query.start,
         });
         if (allowRedispatch && feats.length) {
-            let minStart = Infinity;
-            let maxEnd = -Infinity;
+            let minStart = Number.POSITIVE_INFINITY;
+            let maxEnd = Number.NEGATIVE_INFINITY;
             for (const feat of feats) {
                 if (feat.start < minStart) {
                     minStart = feat.start;

package/esm/index.js

@@ -26,7 +26,7 @@ export default class BedPlugin extends Plugin {
                 if (regexGuess.test(fileName) && !adapterHint) {
                     return obj;
                 }
-                else if (adapterHint === adapterName) {
+                if (adapterHint === adapterName) {
                     return obj;
                 }
                 return adapterGuesser(file, index, adapterHint);

package/esm/util.d.ts

@@ -30,9 +30,9 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     start: number;
     uniqueId: string;
     refName: string;
-    chromStarts: number[];
+    chromStarts?: number[];
     blockSizes: number[];
-    blockStarts: number[];
+    blockStarts?: number[];
 }): {
     uniqueId: string;
     start: number;

package/esm/util.js

@@ -1,14 +1,14 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 export function ucscProcessedTranscript(feature) {
-    var _a;
     const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
     if (!thickStart || !thickEnd || !strand) {
         return feature;
     }
     const subfeatures = [];
-    (_a = oldSubfeatures
+    oldSubfeatures
         .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start)) === null || _a === void 0 ? void 0 : _a.forEach(block => {
+        .sort((a, b) => a.start - b.start)
+        .forEach(block => {
         const start = block.start;
         const end = block.end;
         if (thickStart >= end) {
@@ -55,7 +55,7 @@ export function ucscProcessedTranscript(feature) {
                 end: thickStart,
                 refName,
             }, {
-                type: `CDS`,
+                type: 'CDS',
                 start: thickStart,
                 end: thickEnd,
                 refName,
@@ -70,7 +70,7 @@ export function ucscProcessedTranscript(feature) {
             // CDS | UTR
             const prime = strand > 0 ? 'three' : 'five';
             subfeatures.push({
-                type: `CDS`,
+                type: 'CDS',
                 start,
                 end: thickEnd,
                 refName,
@@ -95,15 +95,16 @@ export function ucscProcessedTranscript(feature) {
     return { ...rest, strand, type: 'mRNA', refName, subfeatures };
 }
 function defaultParser(fields, line) {
-    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
+    const obj = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
+    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
     return {
         ...rest,
         blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
         chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
         blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
-        thickStart: +thickStart,
-        thickEnd: +thickEnd,
-        blockCount: +blockCount,
+        thickStart: thickStart ? +thickStart : undefined,
+        thickEnd: thickEnd ? +thickEnd : undefined,
+        blockCount: blockCount ? +blockCount : undefined,
     };
 }
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
@@ -111,7 +112,7 @@ export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount,
     const starts = chromStarts || blockStarts || [];
     for (let b = 0; b < blockCount; b++) {
         const bmin = (starts[b] || 0) + start;
-        const bmax = bmin + ((blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b]) || 0);
+        const bmax = bmin + (blockSizes[b] || 0);
         subfeatures.push({
             uniqueId: `${uniqueId}-${b}`,
             start: bmin,
@@ -157,11 +158,11 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
         id: uniqueId,
         data: isUcscProcessedTranscript(data)
             ? ucscProcessedTranscript({
-                thickStart,
-                thickEnd,
-                blockCount,
-                blockSizes,
-                chromStarts,
+                thickStart: thickStart,
+                thickEnd: thickEnd,
+                blockCount: blockCount,
+                blockSizes: blockSizes,
+                chromStarts: chromStarts,
                 ...f,
             })
             : f,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/bed",
+    "test": "cd ../..; jest --passWithNoTests plugins/bed",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^4.0.0",
+    "@gmod/bbi": "^5.0.0",
     "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.6"
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }