@jbrowse/plugin-gff3 2.13.1 → 2.14.0

package/dist/Gff3Adapter/Gff3Adapter.d.ts

@@ -2,17 +2,18 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+type StatusCallback = (arg: string) => void;
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
-    protected gffFeatures?: Promise<{
+    gffFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, ((sc?: (arg: string) => void) => IntervalTree) | undefined>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     private loadDataP;
     private loadData;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private featureData;
     freeResources(): void;
 }
+export {};

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -10,10 +10,8 @@ const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const gff_1 = __importDefault(require("@gmod/gff"));
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+const util_1 = require("@jbrowse/core/util");
+const featureData_1 = require("../featureData");
 class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -21,12 +19,14 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const pm = this.pluginManager;
-        const buf = await (0, io_1.openLocation)(this.getConf('gffLocation'), pm).readFile();
-        const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        const buf = (await (0, io_1.openLocation)(this.getConf('gffLocation'), this.pluginManager).readFile(opts));
+        const buffer = (0, util_1.isGzip)(buf)
+            ? await (0, util_1.updateStatus)('Unzipping', statusCallback, () => (0, bgzf_filehandle_1.unzip)(buf))
+            : buf;
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
+        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
@@ -46,7 +46,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     if (!featureMap[refName]) {
                         featureMap[refName] = '';
                     }
-                    featureMap[refName] += line + '\n';
+                    featureMap[refName] += `${line}\n`;
                 }
             }
             if (i++ % 10000 === 0) {
@@ -54,38 +54,39 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
             blockStart = n + 1;
         }
-        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => {
-            return [
-                refName,
-                (sc) => {
-                    sc === null || sc === void 0 ? void 0 : sc(`Parsing GFF data`);
-                    if (!this.calculatedIntervalTreeMap[refName]) {
-                        const intervalTree = new interval_tree_1.default();
-                        gff_1.default
-                            .parseStringSync(lines, {
-                            parseFeatures: true,
-                            parseComments: false,
-                            parseDirectives: false,
-                            parseSequences: false,
-                            disableDerivesFromReferences: true,
-                        })
-                            .flat()
-                            .map((f, i) => new simpleFeature_1.default({
-                            data: this.featureData(f),
-                            id: `${this.id}-${refName}-${i}`,
-                        }))
-                            .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
-                        this.calculatedIntervalTreeMap[refName] = intervalTree;
-                    }
-                    return this.calculatedIntervalTreeMap[refName];
-                },
-            ];
-        }));
-        return { header: headerLines.join('\n'), intervalTreeMap };
+        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
+            refName,
+            (sc) => {
+                if (!this.calculatedIntervalTreeMap[refName]) {
+                    sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
+                    const intervalTree = new interval_tree_1.default();
+                    gff_1.default
+                        .parseStringSync(lines, {
+                        parseFeatures: true,
+                        parseComments: false,
+                        parseDirectives: false,
+                        parseSequences: false,
+                        disableDerivesFromReferences: true,
+                    })
+                        .flat()
+                        .map((f, i) => new simpleFeature_1.default({
+                        data: (0, featureData_1.featureData)(f),
+                        id: `${this.id}-${refName}-${i}`,
+                    }))
+                        .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
+                    this.calculatedIntervalTreeMap[refName] = intervalTree;
+                }
+                return this.calculatedIntervalTreeMap[refName];
+            },
+        ]));
+        return {
+            header: headerLines.join('\n'),
+            intervalTreeMap,
+        };
     }
     async loadData(opts) {
         if (!this.gffFeatures) {
-            this.gffFeatures = this.loadDataP(opts).catch(e => {
+            this.gffFeatures = this.loadDataP(opts).catch((e) => {
                 this.gffFeatures = undefined;
                 throw e;
             });
@@ -102,11 +103,13 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a, _b;
+            var _a;
             try {
                 const { start, end, refName } = query;
                 const { intervalTreeMap } = await this.loadData(opts);
-                (_b = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback)) === null || _b === void 0 ? void 0 : _b.search([start, end]).forEach(f => observer.next(f));
+                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
+                    observer.next(f);
+                });
                 observer.complete();
             }
             catch (e) {
@@ -114,68 +117,6 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
         }, opts.signal);
     }
-    featureData(data) {
-        const f = { ...data };
-        f.start -= 1; // convert to interbase
-        if (data.strand === '+') {
-            f.strand = 1;
-        }
-        else if (data.strand === '-') {
-            f.strand = -1;
-        }
-        else if (data.strand === '.') {
-            f.strand = 0;
-        }
-        else {
-            f.strand = undefined;
-        }
-        f.phase = Number(data.phase);
-        f.refName = data.seq_id;
-        if (data.score === null) {
-            delete f.score;
-        }
-        if (data.phase === null) {
-            delete f.score;
-        }
-        const defaultFields = new Set([
-            'start',
-            'end',
-            'seq_id',
-            'score',
-            'type',
-            'source',
-            'phase',
-            'strand',
-        ]);
-        const dataAttributes = data.attributes || {};
-        for (const a of Object.keys(dataAttributes)) {
-            let b = a.toLowerCase();
-            if (defaultFields.has(b)) {
-                // add "suffix" to tag name if it already exists
-                // reproduces behavior of NCList
-                b += '2';
-            }
-            if (dataAttributes[a] !== null) {
-                let attr = dataAttributes[a];
-                if (Array.isArray(attr) && attr.length === 1) {
-                    ;
-                    [attr] = attr;
-                }
-                f[b] = attr;
-            }
-        }
-        f.refName = f.seq_id;
-        // the SimpleFeature constructor takes care of recursively inflating subfeatures
-        if (data.child_features && data.child_features.length > 0) {
-            f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
-        }
-        delete f.child_features;
-        delete f.data;
-        // delete f.derived_features
-        delete f.attributes;
-        delete f.seq_id;
-        return f;
-    }
     freeResources( /* { region } */) { }
 }
 exports.default = Gff3Adapter;

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -15,6 +15,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     private getFeaturesHelper;
     private parseLine;
     private formatFeatures;
-    private featureData;
     freeResources(): void;
 }

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable no-underscore-dangle */
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const range_1 = require("@jbrowse/core/util/range");
 const io_1 = require("@jbrowse/core/util/io");
@@ -12,6 +11,7 @@ const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeatur
 const tabix_1 = require("@gmod/tabix");
 const gff_1 = __importDefault(require("@gmod/gff"));
 const configuration_1 = require("@jbrowse/core/configuration");
+const featureData_1 = require("../featureData");
 class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -44,19 +44,19 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             await this.getFeaturesHelper(query, opts, metadata, observer, true);
         }, opts.signal);
     }
-    async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
+    async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
         try {
             const lines = [];
             await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
                 lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
             });
             if (allowRedispatch && lines.length) {
-                let minStart = Infinity;
-                let maxEnd = -Infinity;
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
                 lines.forEach(line => {
                     const featureType = line.fields[2];
-                    // only expand redispatch range if feature is not a "dontRedispatch" type
-                    // skips large regions like chromosome,region
+                    // only expand redispatch range if feature is not a "dontRedispatch"
+                    // type skips large regions like chromosome,region
                     if (!this.dontRedispatch.includes(featureType)) {
                         const start = line.start - 1; // gff is 1-based
                         if (start < minStart) {
@@ -94,11 +94,13 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 parseSequences: false,
                 disableDerivesFromReferences: true,
             });
-            features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
-                if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
-                    observer.next(f);
-                }
-            }));
+            features.forEach(featureLocs => {
+                this.formatFeatures(featureLocs).forEach(f => {
+                    if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
+                        observer.next(f);
+                    }
+                });
+            });
             observer.complete();
         }
         catch (e) {
@@ -116,73 +118,13 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     formatFeatures(featureLocs) {
-        return featureLocs.map(featureLoc => new simpleFeature_1.default({
-            data: this.featureData(featureLoc),
-            id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
-        }));
-    }
-    featureData(data) {
-        const f = { ...data };
-        f.start -= 1; // convert to interbase
-        if (data.strand === '+') {
-            f.strand = 1;
-        }
-        else if (data.strand === '-') {
-            f.strand = -1;
-        }
-        else if (data.strand === '.') {
-            f.strand = 0;
-        }
-        else {
-            f.strand = undefined;
-        }
-        f.phase = Number(data.phase);
-        f.refName = data.seq_id;
-        if (data.score === null) {
-            delete f.score;
-        }
-        if (data.phase === null) {
-            delete f.score;
-        }
-        const defaultFields = new Set([
-            'start',
-            'end',
-            'seq_id',
-            'score',
-            'type',
-            'source',
-            'phase',
-            'strand',
-        ]);
-        const dataAttributes = data.attributes || {};
-        for (const a of Object.keys(dataAttributes)) {
-            let b = a.toLowerCase();
-            if (defaultFields.has(b)) {
-                // add "suffix" to tag name if it already exists
-                // reproduces behavior of NCList
-                b += '2';
-            }
-            if (dataAttributes[a] !== null) {
-                let attr = dataAttributes[a];
-                if (Array.isArray(attr) && attr.length === 1) {
-                    ;
-                    [attr] = attr;
-                }
-                f[b] = attr;
-            }
-        }
-        f.refName = f.seq_id;
-        // the SimpleFeature constructor takes care of recursively inflating subfeatures
-        if (data.child_features && data.child_features.length > 0) {
-            f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
-        }
-        delete f.child_features;
-        delete f.data;
-        // delete f.derived_features
-        delete f._linehash;
-        delete f.attributes;
-        delete f.seq_id;
-        return f;
+        return featureLocs.map(featureLoc => {
+            var _a, _b;
+            return new simpleFeature_1.default({
+                data: (0, featureData_1.featureData)(featureLoc),
+                id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
+            });
+        });
     }
     freeResources( /* { region } */) { }
 }

package/dist/GuessGff3/index.js

@@ -35,7 +35,7 @@ function GuessGff3F(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);

package/dist/featureData.d.ts

@@ -0,0 +1,2 @@
+import { GFF3FeatureLineWithRefs } from '@gmod/gff';
+export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;

package/dist/featureData.js

@@ -0,0 +1,64 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = featureData;
+function featureData(data) {
+    const f = { ...data };
+    f.start -= 1; // convert to interbase
+    if (data.strand === '+') {
+        f.strand = 1;
+    }
+    else if (data.strand === '-') {
+        f.strand = -1;
+    }
+    else if (data.strand === '.') {
+        f.strand = 0;
+    }
+    else {
+        f.strand = undefined;
+    }
+    f.phase = data.phase === null ? undefined : Number(data.phase);
+    f.refName = data.seq_id;
+    if (data.score === null) {
+        f.score = undefined;
+    }
+    const defaultFields = new Set([
+        'start',
+        'end',
+        'seq_id',
+        'score',
+        'type',
+        'source',
+        'phase',
+        'strand',
+    ]);
+    const dataAttributes = data.attributes || {};
+    for (const a of Object.keys(dataAttributes)) {
+        let b = a.toLowerCase();
+        if (defaultFields.has(b)) {
+            // add "suffix" to tag name if it already exists
+            // reproduces behavior of NCList
+            b += '2';
+        }
+        if (dataAttributes[a]) {
+            let attr = dataAttributes[a];
+            if (Array.isArray(attr) && attr.length === 1) {
+                ;
+                [attr] = attr;
+            }
+            f[b] = attr;
+        }
+    }
+    f.refName = f.seq_id;
+    // the SimpleFeature constructor takes care of recursively inflating
+    // subfeatures
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    if (data.child_features && data.child_features.length > 0) {
+        f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
+    }
+    f.child_features = undefined;
+    f.data = undefined;
+    // delete f.derived_features
+    f.attributes = undefined;
+    f.seq_id = undefined;
+    return f;
+}

package/esm/Gff3Adapter/Gff3Adapter.d.ts

@@ -2,17 +2,18 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+type StatusCallback = (arg: string) => void;
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
-    protected gffFeatures?: Promise<{
+    gffFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, ((sc?: (arg: string) => void) => IntervalTree) | undefined>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     private loadDataP;
     private loadData;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private featureData;
     freeResources(): void;
 }
+export {};

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -5,10 +5,8 @@ import IntervalTree from '@flatten-js/interval-tree';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { unzip } from '@gmod/bgzf-filehandle';
 import gff from '@gmod/gff';
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+import { isGzip, updateStatus } from '@jbrowse/core/util';
+import { featureData } from '../featureData';
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -16,12 +14,14 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const pm = this.pluginManager;
-        const buf = await openLocation(this.getConf('gffLocation'), pm).readFile();
-        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        const buf = (await openLocation(this.getConf('gffLocation'), this.pluginManager).readFile(opts));
+        const buffer = isGzip(buf)
+            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
+            : buf;
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
+        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
@@ -41,7 +41,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
                     if (!featureMap[refName]) {
                         featureMap[refName] = '';
                     }
-                    featureMap[refName] += line + '\n';
+                    featureMap[refName] += `${line}\n`;
                 }
             }
             if (i++ % 10000 === 0) {
@@ -49,38 +49,39 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
             }
             blockStart = n + 1;
         }
-        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => {
-            return [
-                refName,
-                (sc) => {
-                    sc === null || sc === void 0 ? void 0 : sc(`Parsing GFF data`);
-                    if (!this.calculatedIntervalTreeMap[refName]) {
-                        const intervalTree = new IntervalTree();
-                        gff
-                            .parseStringSync(lines, {
-                            parseFeatures: true,
-                            parseComments: false,
-                            parseDirectives: false,
-                            parseSequences: false,
-                            disableDerivesFromReferences: true,
-                        })
-                            .flat()
-                            .map((f, i) => new SimpleFeature({
-                            data: this.featureData(f),
-                            id: `${this.id}-${refName}-${i}`,
-                        }))
-                            .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
-                        this.calculatedIntervalTreeMap[refName] = intervalTree;
-                    }
-                    return this.calculatedIntervalTreeMap[refName];
-                },
-            ];
-        }));
-        return { header: headerLines.join('\n'), intervalTreeMap };
+        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
+            refName,
+            (sc) => {
+                if (!this.calculatedIntervalTreeMap[refName]) {
+                    sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
+                    const intervalTree = new IntervalTree();
+                    gff
+                        .parseStringSync(lines, {
+                        parseFeatures: true,
+                        parseComments: false,
+                        parseDirectives: false,
+                        parseSequences: false,
+                        disableDerivesFromReferences: true,
+                    })
+                        .flat()
+                        .map((f, i) => new SimpleFeature({
+                        data: featureData(f),
+                        id: `${this.id}-${refName}-${i}`,
+                    }))
+                        .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
+                    this.calculatedIntervalTreeMap[refName] = intervalTree;
+                }
+                return this.calculatedIntervalTreeMap[refName];
+            },
+        ]));
+        return {
+            header: headerLines.join('\n'),
+            intervalTreeMap,
+        };
     }
     async loadData(opts) {
         if (!this.gffFeatures) {
-            this.gffFeatures = this.loadDataP(opts).catch(e => {
+            this.gffFeatures = this.loadDataP(opts).catch((e) => {
                 this.gffFeatures = undefined;
                 throw e;
             });
@@ -97,11 +98,13 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
-            var _a, _b;
+            var _a;
             try {
                 const { start, end, refName } = query;
                 const { intervalTreeMap } = await this.loadData(opts);
-                (_b = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback)) === null || _b === void 0 ? void 0 : _b.search([start, end]).forEach(f => observer.next(f));
+                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
+                    observer.next(f);
+                });
                 observer.complete();
             }
             catch (e) {
@@ -109,67 +112,5 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
             }
         }, opts.signal);
     }
-    featureData(data) {
-        const f = { ...data };
-        f.start -= 1; // convert to interbase
-        if (data.strand === '+') {
-            f.strand = 1;
-        }
-        else if (data.strand === '-') {
-            f.strand = -1;
-        }
-        else if (data.strand === '.') {
-            f.strand = 0;
-        }
-        else {
-            f.strand = undefined;
-        }
-        f.phase = Number(data.phase);
-        f.refName = data.seq_id;
-        if (data.score === null) {
-            delete f.score;
-        }
-        if (data.phase === null) {
-            delete f.score;
-        }
-        const defaultFields = new Set([
-            'start',
-            'end',
-            'seq_id',
-            'score',
-            'type',
-            'source',
-            'phase',
-            'strand',
-        ]);
-        const dataAttributes = data.attributes || {};
-        for (const a of Object.keys(dataAttributes)) {
-            let b = a.toLowerCase();
-            if (defaultFields.has(b)) {
-                // add "suffix" to tag name if it already exists
-                // reproduces behavior of NCList
-                b += '2';
-            }
-            if (dataAttributes[a] !== null) {
-                let attr = dataAttributes[a];
-                if (Array.isArray(attr) && attr.length === 1) {
-                    ;
-                    [attr] = attr;
-                }
-                f[b] = attr;
-            }
-        }
-        f.refName = f.seq_id;
-        // the SimpleFeature constructor takes care of recursively inflating subfeatures
-        if (data.child_features && data.child_features.length > 0) {
-            f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
-        }
-        delete f.child_features;
-        delete f.data;
-        // delete f.derived_features
-        delete f.attributes;
-        delete f.seq_id;
-        return f;
-    }
     freeResources( /* { region } */) { }
 }

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -15,6 +15,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     private getFeaturesHelper;
     private parseLine;
     private formatFeatures;
-    private featureData;
     freeResources(): void;
 }

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -1,4 +1,3 @@
-/* eslint-disable no-underscore-dangle */
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -7,6 +6,7 @@ import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
 import gff from '@gmod/gff';
 import { readConfObject, } from '@jbrowse/core/configuration';
+import { featureData } from '../featureData';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -39,19 +39,19 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             await this.getFeaturesHelper(query, opts, metadata, observer, true);
         }, opts.signal);
     }
-    async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
+    async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
         try {
             const lines = [];
             await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
                 lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
             });
             if (allowRedispatch && lines.length) {
-                let minStart = Infinity;
-                let maxEnd = -Infinity;
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
                 lines.forEach(line => {
                     const featureType = line.fields[2];
-                    // only expand redispatch range if feature is not a "dontRedispatch" type
-                    // skips large regions like chromosome,region
+                    // only expand redispatch range if feature is not a "dontRedispatch"
+                    // type skips large regions like chromosome,region
                     if (!this.dontRedispatch.includes(featureType)) {
                         const start = line.start - 1; // gff is 1-based
                         if (start < minStart) {
@@ -89,11 +89,13 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                 parseSequences: false,
                 disableDerivesFromReferences: true,
             });
-            features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
-                if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
-                    observer.next(f);
-                }
-            }));
+            features.forEach(featureLocs => {
+                this.formatFeatures(featureLocs).forEach(f => {
+                    if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
+                        observer.next(f);
+                    }
+                });
+            });
             observer.complete();
         }
         catch (e) {
@@ -111,73 +113,13 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
         };
     }
     formatFeatures(featureLocs) {
-        return featureLocs.map(featureLoc => new SimpleFeature({
-            data: this.featureData(featureLoc),
-            id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
-        }));
-    }
-    featureData(data) {
-        const f = { ...data };
-        f.start -= 1; // convert to interbase
-        if (data.strand === '+') {
-            f.strand = 1;
-        }
-        else if (data.strand === '-') {
-            f.strand = -1;
-        }
-        else if (data.strand === '.') {
-            f.strand = 0;
-        }
-        else {
-            f.strand = undefined;
-        }
-        f.phase = Number(data.phase);
-        f.refName = data.seq_id;
-        if (data.score === null) {
-            delete f.score;
-        }
-        if (data.phase === null) {
-            delete f.score;
-        }
-        const defaultFields = new Set([
-            'start',
-            'end',
-            'seq_id',
-            'score',
-            'type',
-            'source',
-            'phase',
-            'strand',
-        ]);
-        const dataAttributes = data.attributes || {};
-        for (const a of Object.keys(dataAttributes)) {
-            let b = a.toLowerCase();
-            if (defaultFields.has(b)) {
-                // add "suffix" to tag name if it already exists
-                // reproduces behavior of NCList
-                b += '2';
-            }
-            if (dataAttributes[a] !== null) {
-                let attr = dataAttributes[a];
-                if (Array.isArray(attr) && attr.length === 1) {
-                    ;
-                    [attr] = attr;
-                }
-                f[b] = attr;
-            }
-        }
-        f.refName = f.seq_id;
-        // the SimpleFeature constructor takes care of recursively inflating subfeatures
-        if (data.child_features && data.child_features.length > 0) {
-            f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
-        }
-        delete f.child_features;
-        delete f.data;
-        // delete f.derived_features
-        delete f._linehash;
-        delete f.attributes;
-        delete f.seq_id;
-        return f;
+        return featureLocs.map(featureLoc => {
+            var _a, _b;
+            return new SimpleFeature({
+                data: featureData(featureLoc),
+                id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
+            });
+        });
     }
     freeResources( /* { region } */) { }
 }

package/esm/GuessGff3/index.js

@@ -32,7 +32,7 @@ export default function GuessGff3F(pluginManager) {
             if (regexGuess.test(fileName) && !adapterHint) {
                 return obj;
             }
-            else if (adapterHint === adapterName) {
+            if (adapterHint === adapterName) {
                 return obj;
             }
             return adapterGuesser(file, index, adapterHint);

package/esm/featureData.d.ts

@@ -0,0 +1,2 @@
+import { GFF3FeatureLineWithRefs } from '@gmod/gff';
+export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;

package/esm/featureData.js

@@ -0,0 +1,61 @@
+export function featureData(data) {
+    const f = { ...data };
+    f.start -= 1; // convert to interbase
+    if (data.strand === '+') {
+        f.strand = 1;
+    }
+    else if (data.strand === '-') {
+        f.strand = -1;
+    }
+    else if (data.strand === '.') {
+        f.strand = 0;
+    }
+    else {
+        f.strand = undefined;
+    }
+    f.phase = data.phase === null ? undefined : Number(data.phase);
+    f.refName = data.seq_id;
+    if (data.score === null) {
+        f.score = undefined;
+    }
+    const defaultFields = new Set([
+        'start',
+        'end',
+        'seq_id',
+        'score',
+        'type',
+        'source',
+        'phase',
+        'strand',
+    ]);
+    const dataAttributes = data.attributes || {};
+    for (const a of Object.keys(dataAttributes)) {
+        let b = a.toLowerCase();
+        if (defaultFields.has(b)) {
+            // add "suffix" to tag name if it already exists
+            // reproduces behavior of NCList
+            b += '2';
+        }
+        if (dataAttributes[a]) {
+            let attr = dataAttributes[a];
+            if (Array.isArray(attr) && attr.length === 1) {
+                ;
+                [attr] = attr;
+            }
+            f[b] = attr;
+        }
+    }
+    f.refName = f.seq_id;
+    // the SimpleFeature constructor takes care of recursively inflating
+    // subfeatures
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    if (data.child_features && data.child_features.length > 0) {
+        f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
+    }
+    f.child_features = undefined;
+    f.data = undefined;
+    // delete f.derived_features
+    f.attributes = undefined;
+    f.seq_id = undefined;
+    return f;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "2.13.1",
+  "version": "2.14.0",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/gff3 --passWithNoTests",
+    "test": "cd ../..; jest --passWithNoTests plugins/gff3 --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }