@jbrowse/plugin-gff3 2.16.1 → 2.18.0

package/dist/Gff3Adapter/Gff3Adapter.d.ts

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -3,14 +3,13 @@ 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 BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-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_nostream_1 = require("gff-nostream");
-const util_1 = require("@jbrowse/core/util");
 const featureData_1 = require("../featureData");
 class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -19,20 +18,16 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        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 buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('gffLocation'), this.pluginManager));
         const headerLines = [];
         const featureMap = {};
+        const decoder = new TextDecoder('utf8');
         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);
-            // could be a non-newline ended file, so subarray to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);
@@ -108,8 +103,8 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = Gff3Adapter;

package/dist/Gff3Adapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gffLocation: {
         type: string;
         defaultValue: {

package/dist/Gff3Adapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config Gff3Adapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const Gff3Adapter = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
-    /**
-     * #slot
-     */
     gffLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },

package/dist/Gff3Adapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function Gff3AdapterF(pluginManager: PluginManager): void;

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     protected gff: TabixIndexedFile;
     protected dontRedispatch: string[];

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -3,14 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const tabix_1 = require("@gmod/tabix");
+const configuration_1 = require("@jbrowse/core/configuration");
 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");
+const range_1 = require("@jbrowse/core/util/range");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const tabix_1 = require("@gmod/tabix");
 const gff_nostream_1 = require("gff-nostream");
-const configuration_1 = require("@jbrowse/core/configuration");
 const featureData_1 = require("../featureData");
 class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -42,7 +42,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const metadata = await this.gff.getMetadata();
             await this.getFeaturesHelper(query, opts, metadata, observer, true);
-        }, opts.signal);
+        }, opts.stopToken);
     }
     async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
         var _a, _b;
@@ -56,10 +56,8 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 let maxEnd = Number.NEGATIVE_INFINITY;
                 for (const line of lines) {
                     const featureType = line.fields[2];
-                    // 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
+                        const start = line.start - 1;
                         if (start < minStart) {
                             minStart = start;
                         }
@@ -69,8 +67,6 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }
                 }
                 if (maxEnd > query.end || minStart < query.start) {
-                    // make a new feature callback to only return top-level features
-                    // in the original query range
                     await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
                     return;
                 }
@@ -107,7 +103,6 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     parseLine(columnNumbers, line, fileOffset) {
         const fields = line.split('\t');
-        // note: index column numbers are 1-based
         return {
             start: +fields[columnNumbers.start - 1],
             end: +fields[columnNumbers.end - 1],
@@ -115,6 +110,6 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields,
         };
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = Gff3TabixAdapter;

package/dist/Gff3TabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gffGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.indexType
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,13 +20,6 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we requested.
-     * you can disable this for certain feature types to avoid fetching e.g. the
-     * entire chromosome
-     */
     dontRedispatch: {
         type: string;
         defaultValue: string[];

package/dist/Gff3TabixAdapter/configSchema.js

@@ -1,32 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config Gff3TabixAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
 const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
-    /**
-     * #slot
-     */
     gffGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('Gff3TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.indexType
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -35,13 +22,6 @@ const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdap
             },
         },
     }),
-    /**
-     * #slot
-     * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we requested.
-     * you can disable this for certain feature types to avoid fetching e.g. the
-     * entire chromosome
-     */
     dontRedispatch: {
         type: 'stringArray',
         defaultValue: ['chromosome', 'region', 'contig'],

package/dist/Gff3TabixAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function Gff3TabixAdapterF(pluginManager: PluginManager): void;

package/dist/GuessGff3/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function GuessGff3F(pluginManager: PluginManager): void;

package/dist/featureData.d.ts

@@ -1,4 +1,4 @@
-import { GFF3FeatureLineWithRefs } from 'gff-nostream';
+import type { GFF3FeatureLineWithRefs } from 'gff-nostream';
 interface GFF3Feature {
     start: number;
     end: number;

package/dist/featureData.js

@@ -28,8 +28,6 @@ function featureData(data) {
     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] && a !== '_lineHash') {

package/dist/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class GFF3Plugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const Gff3TabixAdapter_1 = __importDefault(require("./Gff3TabixAdapter"));
 const Gff3Adapter_1 = __importDefault(require("./Gff3Adapter"));
+const Gff3TabixAdapter_1 = __importDefault(require("./Gff3TabixAdapter"));
 const GuessGff3_1 = __importDefault(require("./GuessGff3"));
 class GFF3Plugin extends Plugin_1.default {
     constructor() {

package/esm/Gff3Adapter/Gff3Adapter.d.ts

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -1,11 +1,10 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import IntervalTree from '@flatten-js/interval-tree';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { unzip } from '@gmod/bgzf-filehandle';
 import { parseStringSync } from 'gff-nostream';
-import { isGzip, updateStatus } from '@jbrowse/core/util';
 import { featureData } from '../featureData';
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -14,20 +13,16 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('gffLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('gffLocation'), this.pluginManager));
         const headerLines = [];
         const featureMap = {};
+        const decoder = new TextDecoder('utf8');
         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);
-            // could be a non-newline ended file, so subarray to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);
@@ -103,7 +98,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/Gff3Adapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gffLocation: {
         type: string;
         defaultValue: {

package/esm/Gff3Adapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config Gff3Adapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const Gff3Adapter = ConfigurationSchema('Gff3Adapter', {
-    /**
-     * #slot
-     */
     gffLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },

package/esm/Gff3Adapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function Gff3AdapterF(pluginManager: PluginManager): void;

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     protected gff: TabixIndexedFile;
     protected dontRedispatch: string[];

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -1,11 +1,11 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
+import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { TabixIndexedFile } from '@gmod/tabix';
 import { parseStringSync } from 'gff-nostream';
-import { readConfObject, } from '@jbrowse/core/configuration';
 import { featureData } from '../featureData';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -37,7 +37,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const metadata = await this.gff.getMetadata();
             await this.getFeaturesHelper(query, opts, metadata, observer, true);
-        }, opts.signal);
+        }, opts.stopToken);
     }
     async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
         var _a, _b;
@@ -51,10 +51,8 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                 let maxEnd = Number.NEGATIVE_INFINITY;
                 for (const line of lines) {
                     const featureType = line.fields[2];
-                    // 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
+                        const start = line.start - 1;
                         if (start < minStart) {
                             minStart = start;
                         }
@@ -64,8 +62,6 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                     }
                 }
                 if (maxEnd > query.end || minStart < query.start) {
-                    // make a new feature callback to only return top-level features
-                    // in the original query range
                     await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
                     return;
                 }
@@ -102,7 +98,6 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     }
     parseLine(columnNumbers, line, fileOffset) {
         const fields = line.split('\t');
-        // note: index column numbers are 1-based
         return {
             start: +fields[columnNumbers.start - 1],
             end: +fields[columnNumbers.end - 1],
@@ -110,5 +105,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             fields,
         };
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/Gff3TabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gffGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.indexType
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,13 +20,6 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we requested.
-     * you can disable this for certain feature types to avoid fetching e.g. the
-     * entire chromosome
-     */
     dontRedispatch: {
         type: string;
         defaultValue: string[];

package/esm/Gff3TabixAdapter/configSchema.js

@@ -1,30 +1,17 @@
-import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config Gff3TabixAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { types } from 'mobx-state-tree';
+function x() { }
 const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
-    /**
-     * #slot
-     */
     gffGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('Gff3TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.indexType
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -33,13 +20,6 @@ const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
             },
         },
     }),
-    /**
-     * #slot
-     * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we requested.
-     * you can disable this for certain feature types to avoid fetching e.g. the
-     * entire chromosome
-     */
     dontRedispatch: {
         type: 'stringArray',
         defaultValue: ['chromosome', 'region', 'contig'],

package/esm/Gff3TabixAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function Gff3TabixAdapterF(pluginManager: PluginManager): void;

package/esm/GuessGff3/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function GuessGff3F(pluginManager: PluginManager): void;

package/esm/GuessGff3/index.js

@@ -1,4 +1,4 @@
-import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default function GuessGff3F(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {

package/esm/featureData.d.ts

@@ -1,4 +1,4 @@
-import { GFF3FeatureLineWithRefs } from 'gff-nostream';
+import type { GFF3FeatureLineWithRefs } from 'gff-nostream';
 interface GFF3Feature {
     start: number;
     end: number;

package/esm/featureData.js

@@ -25,8 +25,6 @@ export function featureData(data) {
     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] && a !== '_lineHash') {

package/esm/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class GFF3Plugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,6 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
-import Gff3TabixAdapterF from './Gff3TabixAdapter';
 import Gff3AdapterF from './Gff3Adapter';
+import Gff3TabixAdapterF from './Gff3TabixAdapter';
 import GuessGff3F from './GuessGff3';
 export default class GFF3Plugin extends Plugin {
     constructor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }