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* misc bug fixes * hub updates * fix unit test
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| Original file line number | Diff line number | Diff line change |
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| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <title>twobit</title> | ||
| </head> | ||
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| <body> | ||
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| <select id="select"> | ||
| <option value=""></option> | ||
| <option value="gorGor4">gorGor4</option> | ||
| <option value="gorGor6">gorGor6</option> | ||
| </select> | ||
| <button id="load-genome">Load genome</button> | ||
| <br> | ||
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| <div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div> | ||
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| <script type="module"> | ||
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| import igv from "../../js/index.js" | ||
| import Hub from "../../js/ucsc/ucscHub.js" | ||
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| const igvConfig = { | ||
| genome: "gorGor4", | ||
| listeners: { | ||
| 'genomechange': ({genome, trackConfigurations}) => { | ||
| console.log('genomechange') | ||
| console.log(genome) | ||
| console.log(trackConfigurations) | ||
| } | ||
| } | ||
| } | ||
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| const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig) | ||
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| document.getElementById("load-genome").addEventListener("click", async () => { | ||
| await browser.loadGenome(document.getElementById("select").value) | ||
| }) | ||
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| </script> | ||
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| </body> | ||
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| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| /** | ||
| * Default chromosome aliases, mostly 1<->chr1 etc. Used if chrom alias file is not supplied. | ||
| * | ||
| */ | ||
| import {isNumber, buildOptions} from "../util/igvUtils.js" | ||
| import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js" | ||
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| class ChromAliasDefaults { | ||
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| aliasRecordCache = new Map() | ||
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| constructor(id, chromosomeNames) { | ||
| this.init(id, chromosomeNames) | ||
| } | ||
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| /** | ||
| * Return the canonical chromosome name for the alias. If none found return the alias | ||
| * | ||
| * @param alias | ||
| * @returns {*} | ||
| */ | ||
| getChromosomeName(alias) { | ||
| return this.aliasRecordCache.has(alias) ? this.aliasRecordCache.get(alias).chr : alias | ||
| } | ||
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| /** | ||
| * Return an alternate chromosome name (alias). | ||
| * | ||
| * @param chr | ||
| * @param nameSet -- The name set, e.g. "ucsc" | ||
| * @returns {*|undefined} | ||
| */ | ||
| getChromosomeAlias(chr, nameSet) | ||
| { | ||
| const aliasRecord = this.aliasRecordCache.get(chr) | ||
| return aliasRecord ? aliasRecord[nameSet] || chr : chr | ||
| } | ||
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| init(id, chromosomeNames) { | ||
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| const aliasRecords = [] | ||
| for (let name of chromosomeNames) { | ||
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| let skipRest = false | ||
| const record = {chr: name} | ||
| aliasRecords.push(record) | ||
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| if (name.startsWith("gi|")) { | ||
| // NCBI | ||
| const alias = ChromAliasDefaults.getNCBIName(name) | ||
| record["ncbi-gi-versioned"] = alias | ||
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| // Also strip version number out, if present | ||
| const dotIndex = alias.lastIndexOf('.') | ||
| if (dotIndex > 0) { | ||
| const alias = alias.substring(0, dotIndex) | ||
| record["ncbi-gi"] = alias | ||
| } | ||
| } else { | ||
| // Special cases for human and mouse | ||
| if (id.startsWith("hg") || id.startsWith("GRCh") || id === "1kg_ref" || id === "b37") { | ||
| switch (name) { | ||
| case "23": | ||
| record["ucsc"] = "chrX" | ||
| skipRest = true | ||
| break | ||
| case "24": | ||
| record["ucsc"] = "chrY" | ||
| skipRest = true | ||
| break | ||
| case "chrX": | ||
| record["ncbi"] = "23" | ||
| skipRest = true | ||
| break | ||
| case "chrY": | ||
| record["ncbi"] = "24" | ||
| skipRest = true | ||
| break | ||
| } | ||
| } else if (id.startsWith("mm") || id.startsWith("GRCm") || id.startsWith("rheMac")) { | ||
| switch (name) { | ||
| case "21": | ||
| record["ucsc"] = "chrX" | ||
| skipRest = true | ||
| break | ||
| case "22": | ||
| record["ucsc"] = "chrY" | ||
| skipRest = true | ||
| break | ||
| case "chrX": | ||
| record["ncbi"] = "21" | ||
| skipRest = true | ||
| break | ||
| case "chrY": | ||
| record["ncbi"] = "22" | ||
| skipRest = true | ||
| break | ||
| } | ||
| } | ||
| if (skipRest) continue | ||
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| // | ||
| if (name === "chrM") { | ||
| record["ncbi"] = "MT" | ||
| } else if (name === "MT") { | ||
| record["ucsc"] = "chrM" | ||
| } else if (name.toLowerCase().startsWith("chr")) { | ||
| record["ncbi"] = name.substring(3) | ||
| } else if (Number.isInteger(Number(name))) { | ||
| record["ucsc"] = "chr" + name | ||
| } | ||
| } | ||
| } | ||
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| for (let rec of aliasRecords) { | ||
| for (let a of Object.values(rec)) { | ||
| this.aliasRecordCache.set(a, rec) | ||
| } | ||
| } | ||
| } | ||
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| search(alias) { | ||
| return this.aliasRecordCache.get(alias) | ||
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| } | ||
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| /** | ||
| * Extract the user friendly name from an NCBI accession | ||
| * example: gi|125745044|ref|NC_002229.3| => NC_002229.3 | ||
| */ | ||
| static getNCBIName(name) { | ||
| const tokens = name.split("\\|") | ||
| return tokens[tokens.length - 1] | ||
| } | ||
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| } | ||
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| export default ChromAliasDefaults |
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