@jbrowse/img 2.10.1 → 2.10.3

package/README.md

@@ -26,9 +26,6 @@ your path
 npm install -g @jbrowse/img
 ```
 
-If you are using npm version 7+ (released 2021) you may also need to add
-`--legacy-peer-deps`
-
 If you are a developer and want to modify the code, see
 [developer guide](DEVELOPER.md) for details
 
@@ -117,6 +114,14 @@ zoomed too far out. Add force:true to make it render
 jb2export --bam file.bam force:true --loc 1:1,100,000-1,200,000 --fasta hg19.fa
 ```
 
+### Render only the SNPCoverage track of an alignments track
+
+Renders only the snpcov subtrack at height 600 for file.bam
+
+```bash
+jb2export --bam file.bam snpcov height:600
+```
+
 ### Render the sequence track
 
 If you are using the fasta argument, the refseq will be named "refseq" and can

package/dist/index.d.ts

@@ -1 +1 @@
-import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';
+export {};

package/dist/index.js

@@ -1,74 +1,16 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const fs_1 = __importDefault(require("fs"));
 const yargs_1 = __importDefault(require("yargs"));
-require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-const node_fetch_1 = __importStar(require("node-fetch"));
-const jsdom_1 = require("jsdom");
-const canvas_1 = require("canvas");
 // locals
 const parseArgv_1 = require("./parseArgv");
 const renderRegion_1 = require("./renderRegion");
 const util_1 = require("./util");
-// @ts-expect-error
-global.nodeImage = canvas_1.Image;
-// @ts-expect-error
-global.nodeCreateCanvas = canvas_1.createCanvas;
-const { document } = new jsdom_1.JSDOM(`...`).window;
-global.document = document;
-// force use of node-fetch polyfill, even if node 18+ fetch is available.
-// native node 18+ fetch currently gives errors related to unidici and
-// Uint8Array:
-//
-//
-// % node --version
-// v18.12.1
-//
-// % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
-// [
-//   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
-//     '(Use `node --trace-warnings ...` to show where the warning was created)'
-// ]
-// [
-//   RangeError: offset is out of bounds
-//       at Uint8Array.set (<anonymous>)
-//       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
-//       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
-// ]
-// @ts-expect-error
-global.fetch = node_fetch_1.default;
-// @ts-expect-error
-global.Headers = node_fetch_1.Headers;
-// @ts-expect-error
-global.Response = node_fetch_1.Response;
-// @ts-expect-error
-global.Request = node_fetch_1.Request;
+const setupEnv_1 = __importDefault(require("./setupEnv"));
+(0, setupEnv_1.default)();
 const err = console.error;
 console.error = (...p) => {
     if (!`${p[0]}`.match('useLayoutEffect')) {

package/dist/renderRegion.js

@@ -119,7 +119,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
         configData.tracks = [];
     }
     trackList.forEach(track => {
-        const [type, [file]] = track;
+        const [type, opts] = track;
+        const [file] = opts;
         if (type === 'bam') {
             configData.tracks = [
                 ...configData.tracks,
@@ -134,6 +135,16 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                         index: { location: makeLocation(file + '.bai') },
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
+                    ...(opts.includes('snpcov')
+                        ? {
+                            displays: [
+                                {
+                                    type: 'LinearSNPCoverageDisplay',
+                                    displayId: path_1.default.basename(file) + '-' + Math.random(),
+                                },
+                            ],
+                        }
+                        : {}),
                 },
             ];
         }
@@ -151,6 +162,16 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
                         craiLocation: makeLocation(file + '.crai'),
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
+                    ...(opts.includes('snpcov')
+                        ? {
+                            displays: [
+                                {
+                                    type: 'LinearSNPCoverageDisplay',
+                                    displayId: path_1.default.basename(file) + '-' + Math.random(),
+                                },
+                            ],
+                        }
+                        : {}),
                 },
             ];
         }

package/dist/setupEnv.d.ts

@@ -0,0 +1 @@
+export default function setupEnv(): void;

package/dist/setupEnv.js

@@ -0,0 +1,66 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const node_fetch_1 = __importStar(require("node-fetch"));
+const jsdom_1 = require("jsdom");
+const canvas_1 = require("canvas");
+function setupEnv() {
+    // @ts-expect-error
+    global.nodeImage = canvas_1.Image;
+    // @ts-expect-error
+    global.nodeCreateCanvas = canvas_1.createCanvas;
+    const window = new jsdom_1.JSDOM(`...`).window;
+    global.document = window.document;
+    // @ts-expect-error
+    global.window = window;
+    // force use of node-fetch polyfill, even if node 18+ fetch is available.
+    // native node 18+ fetch currently gives errors related to unidici and
+    // Uint8Array:
+    //
+    //
+    // % node --version
+    // v18.12.1
+    //
+    // % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
+    // [
+    //   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
+    //     '(Use `node --trace-warnings ...` to show where the warning was created)'
+    // ]
+    // [
+    //   RangeError: offset is out of bounds
+    //       at Uint8Array.set (<anonymous>)
+    //       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
+    //       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
+    // ]
+    // @ts-expect-error
+    global.fetch = node_fetch_1.default;
+    // @ts-expect-error
+    global.Headers = node_fetch_1.Headers;
+    // @ts-expect-error
+    global.Response = node_fetch_1.Response;
+    // @ts-expect-error
+    global.Request = node_fetch_1.Request;
+}
+exports.default = setupEnv;

package/esm/index.d.ts

@@ -1 +1 @@
-import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';
+export {};

package/esm/index.js

@@ -1,46 +1,11 @@
 import fs from 'fs';
 import yargs from 'yargs';
-import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';
-import fetch, { Headers, Response, Request } from 'node-fetch';
-import { JSDOM } from 'jsdom';
-import { Image, createCanvas } from 'canvas';
 // locals
 import { standardizeArgv, parseArgv } from './parseArgv';
 import { renderRegion } from './renderRegion';
 import { convert } from './util';
-// @ts-expect-error
-global.nodeImage = Image;
-// @ts-expect-error
-global.nodeCreateCanvas = createCanvas;
-const { document } = new JSDOM(`...`).window;
-global.document = document;
-// force use of node-fetch polyfill, even if node 18+ fetch is available.
-// native node 18+ fetch currently gives errors related to unidici and
-// Uint8Array:
-//
-//
-// % node --version
-// v18.12.1
-//
-// % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
-// [
-//   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
-//     '(Use `node --trace-warnings ...` to show where the warning was created)'
-// ]
-// [
-//   RangeError: offset is out of bounds
-//       at Uint8Array.set (<anonymous>)
-//       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
-//       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
-// ]
-// @ts-expect-error
-global.fetch = fetch;
-// @ts-expect-error
-global.Headers = Headers;
-// @ts-expect-error
-global.Response = Response;
-// @ts-expect-error
-global.Request = Request;
+import setupEnv from './setupEnv';
+setupEnv();
 const err = console.error;
 console.error = (...p) => {
     if (!`${p[0]}`.match('useLayoutEffect')) {

package/esm/renderRegion.js

@@ -113,7 +113,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
         configData.tracks = [];
     }
     trackList.forEach(track => {
-        const [type, [file]] = track;
+        const [type, opts] = track;
+        const [file] = opts;
         if (type === 'bam') {
             configData.tracks = [
                 ...configData.tracks,
@@ -128,6 +129,16 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                         index: { location: makeLocation(file + '.bai') },
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
+                    ...(opts.includes('snpcov')
+                        ? {
+                            displays: [
+                                {
+                                    type: 'LinearSNPCoverageDisplay',
+                                    displayId: path.basename(file) + '-' + Math.random(),
+                                },
+                            ],
+                        }
+                        : {}),
                 },
             ];
         }
@@ -145,6 +156,16 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
                         craiLocation: makeLocation(file + '.crai'),
                         sequenceAdapter: configData.assembly.sequence.adapter,
                     },
+                    ...(opts.includes('snpcov')
+                        ? {
+                            displays: [
+                                {
+                                    type: 'LinearSNPCoverageDisplay',
+                                    displayId: path.basename(file) + '-' + Math.random(),
+                                },
+                            ],
+                        }
+                        : {}),
                 },
             ];
         }

package/esm/setupEnv.d.ts

@@ -0,0 +1 @@
+export default function setupEnv(): void;

package/esm/setupEnv.js

@@ -0,0 +1,40 @@
+import fetch, { Headers, Response, Request } from 'node-fetch';
+import { JSDOM } from 'jsdom';
+import { Image, createCanvas } from 'canvas';
+export default function setupEnv() {
+    // @ts-expect-error
+    global.nodeImage = Image;
+    // @ts-expect-error
+    global.nodeCreateCanvas = createCanvas;
+    const window = new JSDOM(`...`).window;
+    global.document = window.document;
+    // @ts-expect-error
+    global.window = window;
+    // force use of node-fetch polyfill, even if node 18+ fetch is available.
+    // native node 18+ fetch currently gives errors related to unidici and
+    // Uint8Array:
+    //
+    //
+    // % node --version
+    // v18.12.1
+    //
+    // % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
+    // [
+    //   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
+    //     '(Use `node --trace-warnings ...` to show where the warning was created)'
+    // ]
+    // [
+    //   RangeError: offset is out of bounds
+    //       at Uint8Array.set (<anonymous>)
+    //       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
+    //       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
+    // ]
+    // @ts-expect-error
+    global.fetch = fetch;
+    // @ts-expect-error
+    global.Headers = Headers;
+    // @ts-expect-error
+    global.Response = Response;
+    // @ts-expect-error
+    global.Request = Request;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.10.1",
+  "version": "2.10.3",
   "main": "dist/index.js",
   "module": "esm/index.js",
   "author": "JBrowse Team",
@@ -16,7 +16,6 @@
     "esm"
   ],
   "scripts": {
-    "test": "cd ../../; jest --env node --testMatch '**/*testmod.js' products/jbrowse-img",
     "clean": "rm -rf dist esm *.tsbuildinfo",
     "prebuild": "yarn clean",
     "build": "npm-run-all build:*",
@@ -28,11 +27,10 @@
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.10.1",
-    "@jbrowse/react-linear-genome-view": "^2.10.1",
-    "abortcontroller-polyfill": "^1.7.3",
+    "@jbrowse/plugin-linear-genome-view": "^2.10.3",
+    "@jbrowse/react-linear-genome-view": "^2.10.3",
     "canvas": "^2.9.1",
-    "jsdom": "^23.0.0",
+    "jsdom": "^24.0.0",
     "mobx": "^6.6.0",
     "node-fetch": "^2.6.7",
     "react": "^18.0.0",
@@ -43,5 +41,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
+  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
 }