@jbrowse/img 2.12.3 → 2.13.0

package/dist/renderRegion.d.ts

@@ -30,6 +30,5 @@ interface Config {
     [key: string]: unknown;
 }
 export declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
-export declare const muiCache: import("@emotion/utils").EmotionCache;
 export declare function renderRegion(opts: Opts): Promise<string>;
 export {};

package/dist/renderRegion.js

@@ -3,18 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.muiCache = void 0;
 exports.readData = readData;
 exports.renderRegion = renderRegion;
-const react_1 = __importDefault(require("react"));
+const client_1 = require("react-dom/client");
 const react_linear_genome_view_1 = require("@jbrowse/react-linear-genome-view");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const cache_1 = __importDefault(require("@emotion/cache"));
-const react_2 = require("@emotion/react");
 const path_1 = __importDefault(require("path"));
 const fs_1 = __importDefault(require("fs"));
 const util_1 = require("./util");
-const client_1 = require("react-dom/client");
 function read(file) {
     let res;
     try {
@@ -121,8 +117,10 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
         configData.tracks = [];
     }
     trackList.forEach(track => {
+        var _a;
         const [type, opts] = track;
-        const [file] = opts;
+        const [file, ...rest] = opts;
+        const index = (_a = rest.find(r => r.startsWith('index:'))) === null || _a === void 0 ? void 0 : _a.replace('index:', '');
         if (type === 'bam') {
             configData.tracks = [
                 ...configData.tracks,
@@ -134,7 +132,10 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                     adapter: {
                         type: 'BamAdapter',
                         bamLocation: makeLocation(file),
-                        index: { location: makeLocation(file + '.bai') },
+                        index: {
+                            location: makeLocation(index || file + '.bai'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'BAI',
+                        },
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
                     ...(opts.includes('snpcov')
@@ -161,7 +162,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                     adapter: {
                         type: 'CramAdapter',
                         cramLocation: makeLocation(file),
-                        craiLocation: makeLocation(file + '.crai'),
+                        craiLocation: makeLocation(index || file + '.crai'),
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
                     ...(opts.includes('snpcov')
@@ -204,7 +205,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                         type: 'VcfTabixAdapter',
                         vcfGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -222,7 +224,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                         type: 'Gff3TabixAdapter',
                         gffGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -270,7 +273,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                         type: 'BedTabixAdapter',
                         bedGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -288,12 +292,6 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
     }
     return configData;
 }
-// without this, the styles can become messed up especially in lgv header
-// xref https://github.com/garronej/tss-react/issues/25
-exports.muiCache = (0, cache_1.default)({
-    key: 'mui',
-    prepend: true,
-});
 function process(trackEntry, view, extra = c => c) {
     const [, [track, ...opts]] = trackEntry;
     const currentTrack = view.showTrack(extra(track));
@@ -393,6 +391,5 @@ async function renderRegion(opts) {
     return (0, plugin_linear_genome_view_1.renderToSvg)(view, {
         rasterizeLayers: !opts.noRasterize,
         ...opts,
-        Wrapper: ({ children }) => (react_1.default.createElement(react_2.CacheProvider, { value: exports.muiCache }, children)),
     });
 }

package/esm/renderRegion.d.ts

@@ -30,6 +30,5 @@ interface Config {
     [key: string]: unknown;
 }
 export declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
-export declare const muiCache: import("@emotion/utils").EmotionCache;
 export declare function renderRegion(opts: Opts): Promise<string>;
 export {};

package/esm/renderRegion.js

@@ -1,12 +1,9 @@
-import React from 'react';
+import { createRoot } from 'react-dom/client';
 import { createViewState } from '@jbrowse/react-linear-genome-view';
 import { renderToSvg, } from '@jbrowse/plugin-linear-genome-view';
-import createCache from '@emotion/cache';
-import { CacheProvider } from '@emotion/react';
 import path from 'path';
 import fs from 'fs';
 import { booleanize } from './util';
-import { createRoot } from 'react-dom/client';
 function read(file) {
     let res;
     try {
@@ -113,8 +110,10 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
         configData.tracks = [];
     }
     trackList.forEach(track => {
+        var _a;
         const [type, opts] = track;
-        const [file] = opts;
+        const [file, ...rest] = opts;
+        const index = (_a = rest.find(r => r.startsWith('index:'))) === null || _a === void 0 ? void 0 : _a.replace('index:', '');
         if (type === 'bam') {
             configData.tracks = [
                 ...configData.tracks,
@@ -126,7 +125,10 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                     adapter: {
                         type: 'BamAdapter',
                         bamLocation: makeLocation(file),
-                        index: { location: makeLocation(file + '.bai') },
+                        index: {
+                            location: makeLocation(index || file + '.bai'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'BAI',
+                        },
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
                     ...(opts.includes('snpcov')
@@ -153,7 +155,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                     adapter: {
                         type: 'CramAdapter',
                         cramLocation: makeLocation(file),
-                        craiLocation: makeLocation(file + '.crai'),
+                        craiLocation: makeLocation(index || file + '.crai'),
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
                     ...(opts.includes('snpcov')
@@ -196,7 +198,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                         type: 'VcfTabixAdapter',
                         vcfGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -214,7 +217,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                         type: 'Gff3TabixAdapter',
                         gffGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -262,7 +266,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                         type: 'BedTabixAdapter',
                         bedGzLocation: makeLocation(file),
                         index: {
-                            location: makeLocation(file + '.tbi'),
+                            location: makeLocation(index || file + '.tbi'),
+                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
                         },
                     },
                 },
@@ -280,12 +285,6 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
     }
     return configData;
 }
-// without this, the styles can become messed up especially in lgv header
-// xref https://github.com/garronej/tss-react/issues/25
-export const muiCache = createCache({
-    key: 'mui',
-    prepend: true,
-});
 function process(trackEntry, view, extra = c => c) {
     const [, [track, ...opts]] = trackEntry;
     const currentTrack = view.showTrack(extra(track));
@@ -385,6 +384,5 @@ export async function renderRegion(opts) {
     return renderToSvg(view, {
         rasterizeLayers: !opts.noRasterize,
         ...opts,
-        Wrapper: ({ children }) => (React.createElement(CacheProvider, { value: muiCache }, children)),
     });
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.12.3",
+  "version": "2.13.0",
   "main": "dist/index.js",
   "module": "esm/index.js",
   "author": "JBrowse Team",
@@ -27,8 +27,8 @@
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.12.3",
-    "@jbrowse/react-linear-genome-view": "^2.12.3",
+    "@jbrowse/plugin-linear-genome-view": "^2.13.0",
+    "@jbrowse/react-linear-genome-view": "^2.13.0",
     "canvas": "^2.9.1",
     "jsdom": "^24.0.0",
     "mobx": "^6.6.0",
@@ -41,5 +41,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2775490221cde56af344acebb0afa7e14531cd81"
+  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
 }