diff --git a/CHANGELOG.md b/CHANGELOG.md index c7fbc87..0f17377 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +v0.2.0 + +- Remove necessity to load the worker script separately +- Remove `workerscriptLocation` option +- Added support for Gnomad SV data +- Added `maxTileWidth` to control who far the user can zoom out. v0.1.0 diff --git a/README.md b/README.md index dd38086..f2fb1b9 100644 --- a/README.md +++ b/README.md @@ -32,14 +32,23 @@ chr21 5030275 . A G . AC0;AS_VQSR AC=0;AN=7910;AF= ``` Note that `AC` (allele count),`AN` (allele number) and `AF` (allele frequency) is required in the INFO column. +The track can also display GnomAD SV (structural variants) data. The entries in the vcf file have to be in the following form + +``` +#CHROM POS ID REF ALT QUAL FILTER INFO +chr3 146453963 nssv16051216 T . . AC=1;AF=4.6e-05;AN=21694;END=146453963;SVLEN=281;SVTYPE=INS +chr3 146480766 nssv15885393 C . . AC=36;AF=0.001659;AN=21694;END=146481132;SVLEN=-367;SVTYPE=DEL +chr3 146485150 nssv15972036 C . . AC=2;AF=9.2e-05;AN=21694;END=146513435;SVLEN=28286;SVTYPE=DUP +chr3 146501411 nssv15885394 T . . AC=38;AF=0.001779;AN=21358;END=146502039;SVLEN=-629;SVTYPE=DEL +``` + + ## Usage -The live scripts can be found at: +The live script can be found at: - https://unpkg.com/higlass-gnomad/dist/higlass-gnomad.min.js -- https://unpkg.com/higlass-gnomad/dist/0.higlass-gnomad.min.worker.js -Note that `higlass-gnomad` currently requires a worker thread. It'll automatically try to retrieve it from the same path as the main script but it needs to be hosted on the same server. The current recommended solution is to pull the already built js files from a release and have your web server serve them from the same path. If you need the worker script to be in a different location than the main script (on the same server), you can use the option `workerScriptLocation` to specify that location. ### Client @@ -62,13 +71,16 @@ The following options are available: "type": "gnomad", "options": { "colorScale": [ - [0.3, 0.3, 0.3, 0.6],// Variant color in RGBA format - [0.6, 0.6, 0.0, 0.7],// Insertion color in RGBA format - [1, 0.0, 0.0, 0.6],// Deletion color in RGBA format + // Variant, Insertion, Deletion, Inversion, Duplication + [0.3, 0.3, 0.3, 0.6], + [0.6, 0.6, 0.0, 0.7], + [1, 0.0, 0.0, 0.55], + [0.68, 0.23, 0.87, 0.8], + [0.27, 0.64, 0.09, 0.8] ], "showMousePosition": false, - "workerScriptLocation": null, // see 'Usage' "variantHeight": 12, // Height of the rectangles + "maxTileWidth": 2e5 // Determines how far the user can zoom out before data loading stops }, "data": { "type": "vcf", diff --git a/package-lock.json b/package-lock.json index 373fda4..8203140 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "higlass-gnomad", - "version": "0.1.2", + "version": "0.2.0", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -218,6 +218,12 @@ } } }, + "@discoveryjs/json-ext": { + "version": "0.5.2", + "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-0.5.2.tgz", + "integrity": "sha512-HyYEUDeIj5rRQU2Hk5HTB2uHsbRQpF70nvMhVzi+VJR0X+xNEhjPui4/kBf3VeH/wqD28PT4sVOm8qqLjBrSZg==", + "dev": true + }, "@gmod/bgzf-filehandle": { "version": "1.3.4", "resolved": "https://registry.npmjs.org/@gmod/bgzf-filehandle/-/bgzf-filehandle-1.3.4.tgz", @@ -271,8 +277,7 @@ "@types/json-schema": { "version": "7.0.6", "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.6.tgz", - "integrity": "sha512-3c+yGKvVP5Y9TYBEibGNR+kLtijnj7mYrXRg+WpFb2X9xm04g/DXYkfg4hmzJQosc9snFNUPkbYIhu+KAm6jJw==", - "dev": true + "integrity": "sha512-3c+yGKvVP5Y9TYBEibGNR+kLtijnj7mYrXRg+WpFb2X9xm04g/DXYkfg4hmzJQosc9snFNUPkbYIhu+KAm6jJw==" }, "@types/json5": { "version": "0.0.29", @@ -281,22 +286,17 @@ "dev": true }, "@types/minimatch": { - "version": "3.0.3", - "resolved": "https://registry.npmjs.org/@types/minimatch/-/minimatch-3.0.3.tgz", - "integrity": "sha512-tHq6qdbT9U1IRSGf14CL0pUlULksvY9OZ+5eEgl1N7t+OA3tGvNpxJCzuKQlsNgCVwbAs670L1vcVQi8j9HjnA==", + "version": "3.0.4", + "resolved": "https://registry.npmjs.org/@types/minimatch/-/minimatch-3.0.4.tgz", + "integrity": "sha512-1z8k4wzFnNjVK/tlxvrWuK5WMt6mydWWP7+zvH5eFep4oj+UkrfiJTRtjCeBXNpwaA/FYqqtb4/QS4ianFpIRA==", "dev": true }, "@types/node": { - "version": "14.14.10", - "resolved": "https://registry.npmjs.org/@types/node/-/node-14.14.10.tgz", - "integrity": "sha512-J32dgx2hw8vXrSbu4ZlVhn1Nm3GbeCFNw2FWL8S5QKucHGY0cyNwjdQdO+KMBZ4wpmC7KhLCiNsdk1RFRIYUQQ==", + "version": "15.3.1", + "resolved": "https://registry.npmjs.org/@types/node/-/node-15.3.1.tgz", + "integrity": "sha512-weaeiP4UF4XgF++3rpQhpIJWsCTS4QJw5gvBhQu6cFIxTwyxWIe3xbnrY/o2lTCQ0lsdb8YIUDUvLR4Vuz5rbw==", "dev": true }, - "@types/zen-observable": { - "version": "0.8.1", - "resolved": "https://registry.npmjs.org/@types/zen-observable/-/zen-observable-0.8.1.tgz", - "integrity": "sha512-wmk0xQI6Yy7Fs/il4EpOcflG4uonUpYGqvZARESLc2oy4u69fkatFLbJOeW4Q6awO15P4rduAe6xkwHevpXcUQ==" - }, "@webassemblyjs/ast": { "version": "1.9.0", "resolved": "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.9.0.tgz", @@ -472,6 +472,27 @@ "@xtuc/long": "4.2.2" } }, + "@webpack-cli/configtest": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/@webpack-cli/configtest/-/configtest-1.0.3.tgz", + "integrity": "sha512-WQs0ep98FXX2XBAfQpRbY0Ma6ADw8JR6xoIkaIiJIzClGOMqVRvPCWqndTxf28DgFopWan0EKtHtg/5W1h0Zkw==", + "dev": true + }, + "@webpack-cli/info": { + "version": "1.2.4", + "resolved": "https://registry.npmjs.org/@webpack-cli/info/-/info-1.2.4.tgz", + "integrity": "sha512-ogE2T4+pLhTTPS/8MM3IjHn0IYplKM4HbVNMCWA9N4NrdPzunwenpCsqKEXyejMfRu6K8mhauIPYf8ZxWG5O6g==", + "dev": true, + "requires": { + "envinfo": "^7.7.3" + } + }, + "@webpack-cli/serve": { + "version": "1.4.0", + "resolved": "https://registry.npmjs.org/@webpack-cli/serve/-/serve-1.4.0.tgz", + "integrity": "sha512-xgT/HqJ+uLWGX+Mzufusl3cgjAcnqYYskaB7o0vRcwOEfuu6hMzSILQpnIzFMGsTaeaX4Nnekl+6fadLbl1/Vg==", + "dev": true + }, "@xtuc/ieee754": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/@xtuc/ieee754/-/ieee754-1.2.0.tgz", @@ -1763,6 +1784,12 @@ "tweetnacl": "^0.14.3" } }, + "before-build-webpack": { + "version": "0.2.11", + "resolved": "https://registry.npmjs.org/before-build-webpack/-/before-build-webpack-0.2.11.tgz", + "integrity": "sha512-xigRuKoJmla3cO/BP76CDlmkXmQFrjlHv6oS16RxmbckYTfi5I3ZBp7MnoKv+C05DqDT1pSl+znLf7pv1Vv4ew==", + "dev": true + }, "big-integer": { "version": "1.6.48", "resolved": "https://registry.npmjs.org/big-integer/-/big-integer-1.6.48.tgz", @@ -1772,8 +1799,7 @@ "big.js": { "version": "5.2.2", "resolved": "https://registry.npmjs.org/big.js/-/big.js-5.2.2.tgz", - "integrity": 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"webpack-plugin-replace": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/webpack-plugin-replace/-/webpack-plugin-replace-1.2.0.tgz", @@ -15280,11 +15282,13 @@ } }, "websocket-driver": { - "version": "0.6.5", - "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.6.5.tgz", - "integrity": "sha1-XLJVbOuF9Dc8bYI4qmkchFThOjY=", + "version": "0.7.4", + "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz", + "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==", "dev": true, "requires": { + "http-parser-js": ">=0.5.1", + "safe-buffer": ">=5.1.0", "websocket-extensions": ">=0.1.1" } }, @@ -15330,6 +15334,12 @@ "string-width": "^1.0.2 || 2" } }, + "wildcard": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.0.tgz", + "integrity": 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"^16.1.0", @@ -49,12 +50,12 @@ "sass-loader": "^7.0.1", "string-replace-loader": "^2.2.0", "style-loader": "^0.20.3", - "threads-plugin": "^1.2.0", - "uglifyjs-webpack-plugin": "^1.2.4", + "threads-plugin": "^1.4.0", + "uglifyjs-webpack-plugin": "^2.2.0", "unminified-webpack-plugin": "^2.0.0", "webpack": "^4.20.2", - "webpack-cli": "^3.1.1", - "webpack-dev-server": "^3.1.1", + "webpack-cli": "^4.0.0", + "webpack-dev-server": "^3.11.2", "webpack-plugin-replace": "^1.2.0", "babel-cli": "^6.26.0", "babel-plugin-transform-object-rest-spread": "^6.26.0", @@ -64,7 +65,7 @@ "scripts": { "build-es": "rm -rf ./es/* && npx babel ./src/ --out-dir ./es/ --env-name esm", "build": "npm run build-es && webpack --mode production", - "start": "webpack-dev-server --mode development --open", + "start": "webpack serve --mode development -c webpack.config.js", "prerelease": "rm -rf dist/*; npm run build; zip -r dist.zip dist" }, "dependencies": { @@ -76,7 +77,9 @@ "d3-scale": "^3.0.1", "higlass-register": "^0.1.0", "lru-cache": "^6.0.0", - "threads": "v1.0.0-beta.6", + "raw-loader": "^4.0.2", + "threads": "v1.6.3", + "sanitize-html": "^2.4.0", "generic-filehandle": "^2.0.2" } } diff --git a/src/GnomadTrack.js b/src/GnomadTrack.js index 90235d8..e4b7b01 100644 --- a/src/GnomadTrack.js +++ b/src/GnomadTrack.js @@ -1,6 +1,8 @@ import VCFDataFetcher from './vcf-fetcher'; -import { spawn, Worker } from 'threads'; +import MyWorkerWeb from 'raw-loader!../dist/worker.js'; +import { spawn, BlobWorker } from 'threads'; import { PILEUP_COLORS } from './vcf-utils'; +import sanitizeHtml from 'sanitize-html'; const createColorTexture = (PIXI, colors) => { const colorTexRes = Math.max(2, Math.ceil(Math.sqrt(colors.length))); @@ -23,27 +25,6 @@ function invY(p, t) { return (p - t.y) / t.k; } -/** - * Get the location of this script so that we can use it to fetch - * the worker script. - * - * @return {String} The url of this script - */ -function getThisScriptLocation() { - const scripts = [...document.getElementsByTagName('script')]; - for (const script of scripts) { - const parts = script.src.split('/'); - - if (parts.length > 0) { - const lastPart = parts[parts.length - 1]; - - if (lastPart.indexOf('higlass-gnomad') >= 0) { - return parts.slice(0, parts.length - 1).join('/'); - } - } - } -} - const scaleScalableGraphics = (graphics, xScale, drawnAtScale) => { const tileK = (drawnAtScale.domain()[1] - drawnAtScale.domain()[0]) / @@ -141,18 +122,9 @@ const GnomadTrack = (HGC, ...args) => { class GnomadTrackClass extends HGC.tracks.Tiled1DPixiTrack { constructor(context, options) { - let baseUrl = `${getThisScriptLocation()}/`; - if (options.workerScriptLocation) { - baseUrl = options.workerScriptLocation; - } - - const worker = spawn( - new Worker('./vcf-fetcher-worker.js', { - _baseURL: baseUrl, - }), - ); - + const worker = spawn(BlobWorker.fromText(MyWorkerWeb)); // this is where the threaded tile fetcher is called + context.dataConfig['maxTileWidth'] = options.maxTileWidth; context.dataFetcher = new VCFDataFetcher(context.dataConfig, worker, HGC); super(context, options); context.dataFetcher.track = this; @@ -264,14 +236,6 @@ const GnomadTrack = (HGC, ...args) => { return [tileMinX, tileMaxX]; } - // colorToArray(color) { - // // const rgb = HGC.libraries.d3Color.rgb(color); - - // // const array = [rgb.r / 255, rgb.g / 255, rgb.b / 255, rgb.opacity]; - // console.log(color) - // return color; - // } - setUpShaderAndTextures() { const colorDict = PILEUP_COLORS; @@ -280,6 +244,8 @@ const GnomadTrack = (HGC, ...args) => { colorDict.VARIANT, colorDict.INSERTION, colorDict.DELETION, + colorDict.INVERSION, + colorDict.DUPLICATION ] = this.options.colorScale.map((x) => x); } @@ -539,6 +505,7 @@ varying vec4 vColor; } getMouseOverHtml(trackX, trackYIn) { + // const trackY = this.valueScaleTransform.invert(track) this.mouseOverGraphics.clear(); // Prevents 'stuck' read outlines when hovering quickly @@ -561,6 +528,8 @@ varying vec4 vColor; let alleleFrequencyHtml = ``; let alleleNumberHtml = ``; let sourceHtml = ``; + let svLength = ``; + const fontStyle = `line-height: 12px;font-family: monospace;font-size:14px;`; for (const variant of filteredList) { @@ -585,16 +554,27 @@ varying vec4 vColor; let vRef = variant.ref.match(/.{1,15}/g).join('
'); let vAlt = variant.alt.match(/.{1,15}/g).join('
'); - variantHtml += `${vRef} → ${vAlt}`; + if(variant.category === "SNV"){ + variantHtml += `${vRef} → ${vAlt}`; + positionHtml += `${variant.chrName}:${ + variant.from - variant.chrOffset + }`; + sourceHtml += `Gnomad`; + } + else { + variantHtml += `Structural variant`; + positionHtml += `${variant.chrName}:${ + variant.from - variant.chrOffset + }-${variant.chrName}:${variant.to - variant.chrOffset}`; + sourceHtml += `Gnomad SV`; + svLength += `${variant.info['SVLEN']}` + } + typeHtml += `${this.capitalizeFirstLetter(variant.type)}`; - positionHtml += `${variant.chrName}:${ - variant.from - variant.chrOffset - }`; alleleCountHtml += `${variant.alleleCount}`; const af = Number.parseFloat(variant.alleleFrequency).toExponential(4); alleleFrequencyHtml += `${af}`; alleleNumberHtml += `${variant.alleleNumber}`; - sourceHtml += `Gnomad`; } @@ -603,14 +583,20 @@ varying vec4 vColor; `` + `${variantHtml}` + `${typeHtml}` + - `${positionHtml}` + + `${positionHtml}`; + + if(svLength.length > 0){ + mouseOverHtml += `${svLength}` + } + + mouseOverHtml += `${alleleCountHtml}` + `${alleleFrequencyHtml}` + `${alleleNumberHtml}` + `${sourceHtml}` + - `
Variant:
Type:
Position:
Position:
SV length:
Allele Count:
Allele Frequency:
Allele Number:
Source:
`; - - return mouseOverHtml; + `
`; + + return sanitizeHtml(mouseOverHtml); } return ''; @@ -642,11 +628,10 @@ varying vec4 vColor; this.tilesetInfo, ); - const DEFAULT_MAX_TILE_WIDTH = 2e5; + const DEFAULT_MAX_TILE_WIDTH = this.options.maxTileWidth || 2e5; if ( - tileWidth > - (this.tilesetInfo.max_tile_width || DEFAULT_MAX_TILE_WIDTH) + tileWidth > DEFAULT_MAX_TILE_WIDTH ) { this.errorTextText = 'Zoom in to see details'; this.drawError(); @@ -720,6 +705,7 @@ varying vec4 vColor; this.drawnAtScale, ); } + this.mouseOverGraphics.clear(); this.animate(); } @@ -793,19 +779,22 @@ GnomadTrack.config = { availableOptions: [ 'colorScale', 'showMousePosition', - 'workerScriptLocation', 'variantHeight', + 'maxTileWidth' // 'minZoom' ], defaultOptions: { colorScale: [ - // Variant, Insertion, Deletion + // Variant, Insertion, Deletion, Inversion, Duplication [0.3, 0.3, 0.3, 0.6], [0.6, 0.6, 0.0, 0.7], - [1, 0.0, 0.0, 0.6], + [1, 0.0, 0.0, 0.55], + [0.68, 0.23, 0.87, 0.8], + [0.27, 0.64, 0.09, 0.8] ], showMousePosition: false, variantHeight: 12, + maxTileWidth: 2e5 }, optionsInfo: { @@ -814,10 +803,12 @@ GnomadTrack.config = { inlineOptions: { default: { value: [ - // Variant, Insertion, Deletion + // Variant, Insertion, Deletion, Inversion, Duplication [0.3, 0.3, 0.3, 0.6], [0.6, 0.6, 0.0, 0.7], - [1, 0.0, 0.0, 0.6], + [1, 0.0, 0.0, 0.55], + [0.68, 0.23, 0.87, 0.8], + [0.27, 0.64, 0.09, 0.8] ], name: 'Default', }, diff --git a/src/index.html b/src/index.html index bc6a3b1..a711f72 100644 --- a/src/index.html +++ b/src/index.html @@ -47,9 +47,8 @@ "views": [ { - "initialXDomain": [10026087.639179552, - 10026405.897125244], - //"initialXDomain": [10000000,10000050], + //"initialXDomain": [10000000, 10050000], + "initialXDomain": [10000000,10000050], @@ -122,11 +121,11 @@ } }, { - "uid": "emty", + "uid": "empty", "type": "empty", "width": 811, "height": 10, - "tilesetUid": "emtyt" + "tilesetUid": "empty" }, { "type": "gnomad", @@ -140,6 +139,28 @@ "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", }, "width": 470 + }, + { + "uid": "empty2", + "type": "empty", + "width": 811, + "height": 10, + "tilesetUid": "empty" + }, + { + "type": "gnomad", + "options": { + "maxTileWidth": 1e8 + }, + "height": 200, + "uid": "gnomad-sv", + "data": { + "type": "vcf", + "vcfUrl": "https://aveit.s3.amazonaws.com/higlass/vcf/gnomad_sv_hg38_higlass.vcf.gz", + "tbiUrl": "https://aveit.s3.amazonaws.com/higlass/vcf/gnomad_sv_hg38_higlass.vcf.gz.tbi", + "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes", + }, + "width": 470 } ], "left": [], diff --git a/src/vcf-fetcher-worker.js b/src/vcf-fetcher-worker.js index 3ab6611..e0ddf22 100644 --- a/src/vcf-fetcher-worker.js +++ b/src/vcf-fetcher-worker.js @@ -120,10 +120,18 @@ function ChromosomeInfo(filepath, success) { /// End Chrominfo ///////////////////////////////////////////////////// +const extractColumnFromVcfInfo = (info, index) => { + const col = {}; + Object.keys(info).forEach((key) => { + col[key] = info[key][index]; + }) + return col; +} + const vcfRecordToJson = (vcfRecord, chrName, chrOffset) => { const segments = []; const info = vcfRecord['INFO']; - + // VCF records can have multiple ALT. We create a segment for each of them vcfRecord['ALT'].forEach((alt, index) => { const segment = { @@ -131,20 +139,42 @@ const vcfRecordToJson = (vcfRecord, chrName, chrOffset) => { alt: alt, ref: vcfRecord.REF, from: vcfRecord.POS + chrOffset, - to: vcfRecord.POS + chrOffset + vcfRecord.REF.length, + to: chrOffset, chrName, chrOffset, alleleCount: info.AC[index], alleleFrequency: info.AF[index], alleleNumber: info.AN[index], + info: extractColumnFromVcfInfo(info, index), row: null, type: 'variant', + category: 'SNV' }; - if (segment['alt'].length > segment['ref'].length) { - segment['type'] = 'insertion'; - } else if (segment['alt'].length < segment['ref'].length) { - segment['type'] = 'deletion'; + // CNVs + if(alt.includes(">")){ + //console.log(vcfRecord); + segment['to'] += info.END[index]; + segment['category'] = 'CNV'; + if(info.SVTYPE[index] === "INS"){ + segment['type'] = 'insertion'; + }else if(info.SVTYPE[index] === "DEL"){ + segment['type'] = 'deletion'; + }else if(info.SVTYPE[index] === "DUP"){ + segment['type'] = 'duplication'; + }else if(info.SVTYPE[index] === "INV"){ + segment['type'] = 'inversion'; + } + //console.log(segment); + } + // SNVs + else{ + segment['to'] += vcfRecord.POS + vcfRecord.REF.length; + if (segment['alt'].length > segment['ref'].length) { + segment['type'] = 'insertion'; + } else if (segment['alt'].length < segment['ref'].length) { + segment['type'] = 'deletion'; + } } segments.push(segment); @@ -169,7 +199,7 @@ const tilesetInfos = {}; // indexed by uuid const dataConfs = {}; -const init = (uid, vcfUrl, tbiUrl, chromSizesUrl) => { +const init = (uid, vcfUrl, tbiUrl, chromSizesUrl, maxTileWidth) => { if (!vcfFiles[vcfUrl]) { vcfFiles[vcfUrl] = new TabixIndexedFile({ filehandle: new RemoteFile(vcfUrl), @@ -195,6 +225,7 @@ const init = (uid, vcfUrl, tbiUrl, chromSizesUrl) => { dataConfs[uid] = { vcfUrl, chromSizesUrl, + maxTileWidth }; }; @@ -228,16 +259,15 @@ const tilesetInfo = (uid) => { }; const tile = async (uid, z, x) => { - const MAX_TILE_WIDTH = 200000; - const { vcfUrl, chromSizesUrl } = dataConfs[uid]; + + const { vcfUrl, chromSizesUrl, maxTileWidth } = dataConfs[uid]; const vcfFile = vcfFiles[vcfUrl]; return tilesetInfo(uid).then((tsInfo) => { const tileWidth = +tsInfo.max_width / 2 ** +z; const recordPromises = []; - if (tileWidth > MAX_TILE_WIDTH) { - // this.errorTextText('Zoomed out too far for this track. Zoomin further to see reads'); + if (tileWidth > maxTileWidth) { return new Promise((resolve) => resolve([])); } @@ -373,6 +403,8 @@ const renderSegments = ( for (const tileId of tileIds) { const tileValue = tileValues.get(`${uid}.${tileId}`); + if(!tileValue) continue + if (tileValue.error) { throw new Error(tileValue.error); } @@ -515,6 +547,10 @@ const renderSegments = ( colorToUse = PILEUP_COLOR_IXS.DELETION; } else if (segment.type === 'insertion') { colorToUse = PILEUP_COLOR_IXS.INSERTION; + } else if (segment.type === 'duplication') { + colorToUse = PILEUP_COLOR_IXS.DUPLICATION; + } else if (segment.type === 'inversion') { + colorToUse = PILEUP_COLOR_IXS.INVERSION; } segment['yTop'] = yTop; addRect( diff --git a/src/vcf-fetcher.js b/src/vcf-fetcher.js index 633edf3..cea6c1e 100644 --- a/src/vcf-fetcher.js +++ b/src/vcf-fetcher.js @@ -24,6 +24,7 @@ class VCFDataFetcher { dataConfig.vcfUrl, dataConfig.tbiUrl, dataConfig.chromSizesUrl, + dataConfig.maxTileWidth ) .then(() => this.worker); }); diff --git a/src/vcf-utils.js b/src/vcf-utils.js index ae07b0a..812aad3 100644 --- a/src/vcf-utils.js +++ b/src/vcf-utils.js @@ -2,7 +2,9 @@ export const PILEUP_COLORS = { VARIANT: [0.3, 0.3, 0.3, 0.6], // gray for the variant background LINE: [0.9, 0.9, 0.9, 1], // gray for the variant background INSERTION: [0.6, 0.6, 0.0, 0.7], - DELETION: [1, 0.0, 0.0, 0.6], + DELETION: [1, 0.0, 0.0, 0.55], + INVERSION: [0.68, 0.23, 0.87, 0.8], + DUPLICATION: [0.27, 0.64, 0.09, 0.8], BLACK: [0, 0, 0, 1], BLACK_05: [0, 0, 0, 0.5], WHITE: [1, 1, 1, 1], diff --git a/webpack.config.js b/webpack.config.js index 21fd0d0..8bd8b62 100644 --- a/webpack.config.js +++ b/webpack.config.js @@ -6,8 +6,44 @@ const OptimizeCssAssetsPlugin = require('optimize-css-assets-webpack-plugin'); const UglifyJsPlugin = require('uglifyjs-webpack-plugin'); const UnminifiedWebpackPlugin = require('unminified-webpack-plugin'); const ThreadsPlugin = require('threads-plugin'); +const WebpackBeforeBuildPlugin = require('before-build-webpack'); +const fs = require('fs'); -module.exports = { +// the WaitPlugin is copypasta from: +// https://www.viget.com/articles/run-multiple-webpack-configs-sequentially/ +class WaitPlugin extends WebpackBeforeBuildPlugin { + constructor(file, interval = 100, timeout = 10000) { + super(function (stats, callback) { + let start = Date.now(); + + function poll() { + if (fs.existsSync(file)) { + callback(); + } else if (Date.now() - start > timeout) { + throw Error( + `Waited too long for the target file (${file}) to be generated. Exiting.`, + ); + } else { + setTimeout(poll, interval); + } + } + + poll(); + }); + } +} + +const workerConfig = { + output: { + filename: 'worker.js', + path: path.resolve(__dirname, 'dist'), + }, + entry: path.resolve(__dirname, 'src/vcf-fetcher-worker'), + target: 'webworker', + plugins: [new UnminifiedWebpackPlugin(), new ThreadsPlugin()], +}; + +const libraryConfig = { output: { filename: 'higlass-gnomad.min.js', library: 'higlass-gnomad', @@ -15,10 +51,11 @@ module.exports = { path: path.resolve(__dirname, 'dist'), }, devServer: { - contentBase: [ - path.join(__dirname, 'node_modules/higlass/dist'), - ], + contentBase: [path.join(__dirname, 'node_modules/higlass/dist')], watchContentBase: true, + writeToDisk: true, + port: 8081, + open: true }, optimization: { minimizer: [ @@ -91,7 +128,7 @@ module.exports = { ], }, }, - 'sass-loader', // compiles Sass to CSS + 'sass-loader', // compiles Sass to CSS ], }, // Extract them HTML files @@ -124,5 +161,8 @@ module.exports = { }), new UnminifiedWebpackPlugin(), new ThreadsPlugin(), + new WaitPlugin('dist/worker.js'), ], }; + +module.exports = [workerConfig, libraryConfig]; \ No newline at end of file