@jbrowse/plugin-gtf 2.16.1 → 2.18.0

package/dist/GtfAdapter/GtfAdapter.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';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/dist/GtfAdapter/GtfAdapter.js

@@ -3,16 +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 util_1 = require("@jbrowse/core/util");
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const gtf_nostream_1 = require("gtf-nostream");
-// locals
 const util_2 = require("../util");
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -20,19 +17,17 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await (0, io_1.openLocation)(this.getConf('gtfLocation'), 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 loc = (0, io_1.openLocation)(this.getConf('gtfLocation'), this.pluginManager);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
         let i = 0;
+        const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice 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 GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = GtfAdapter;

package/dist/GtfAdapter/configSchema.d.ts

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

package/dist/GtfAdapter/configSchema.js

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

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 GtfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -26,10 +26,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const GtfAdapter_1 = require("./GtfAdapter");
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const GtfAdapter_1 = require("./GtfAdapter");
 class GtfPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/dist/util.js

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = featureData;
 function featureData(data) {
     const f = { ...data };
-    f.start -= 1; // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.start -= 1;
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
     f.phase = Number(data.frame);
     f.refName = data.seq_name;
     if (data.score === null) {
@@ -26,15 +26,11 @@ function featureData(data) {
     for (const a of Object.keys(data.attributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
-            // add "suffix" to tag name if it already exists
-            // reproduces behavior of NCList
             b += '2';
         }
         if (data.attributes[a]) {
             let attr = data.attributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
-                // gtf uses double quotes for text values in the attributes column,
-                // remove them
                 attr = attr[0].replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
@@ -42,7 +38,6 @@ function featureData(data) {
     }
     f.refName = f.seq_name;
     f.type = f.featureType;
-    // 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 => featureData(childLoc)));
     }

package/esm/GtfAdapter/GtfAdapter.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';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/esm/GtfAdapter/GtfAdapter.js

@@ -1,13 +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 { SimpleFeature, 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, updateStatus, isGzip, } from '@jbrowse/core/util';
-import { unzip } from '@gmod/bgzf-filehandle';
 import { parseStringSync } from 'gtf-nostream';
-// locals
 import { featureData } from '../util';
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
@@ -15,19 +12,17 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
     }
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('gtfLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const loc = openLocation(this.getConf('gtfLocation'), this.pluginManager);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
         let i = 0;
+        const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice 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 GtfAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/GtfAdapter/configSchema.d.ts

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

package/esm/GtfAdapter/configSchema.js

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

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 GtfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,7 +1,7 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import Plugin from '@jbrowse/core/Plugin';
-import { configSchema as gtfAdapterConfigSchema } from './GtfAdapter';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import { getFileName } from '@jbrowse/core/util/tracks';
+import { configSchema as gtfAdapterConfigSchema } from './GtfAdapter';
 export default class GtfPlugin extends Plugin {
     constructor() {
         super(...arguments);

package/esm/util.js

@@ -1,7 +1,7 @@
 export function featureData(data) {
     const f = { ...data };
-    f.start -= 1; // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.start -= 1;
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
     f.phase = Number(data.frame);
     f.refName = data.seq_name;
     if (data.score === null) {
@@ -23,15 +23,11 @@ export function featureData(data) {
     for (const a of Object.keys(data.attributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
-            // add "suffix" to tag name if it already exists
-            // reproduces behavior of NCList
             b += '2';
         }
         if (data.attributes[a]) {
             let attr = data.attributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
-                // gtf uses double quotes for text values in the attributes column,
-                // remove them
                 attr = attr[0].replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
@@ -39,7 +35,6 @@ export function featureData(data) {
     }
     f.refName = f.seq_name;
     f.type = f.featureType;
-    // 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 => featureData(childLoc)));
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }