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Update deprecated genome reference objects
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+188
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3 files changed

+188
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‎js/browser.js

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@@ -610,7 +610,7 @@ class Browser {
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}
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/**
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* Load a reference genome object. This includes the fasta, and optional cytoband, but no tracks. This method
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* Load a reference genome object. This includes the sequence, and optional cytoband, but no tracks. This method
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* is used by loadGenome and loadSession.
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*
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* @param genomeConfig

‎js/genome/genome.js

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@@ -10,6 +10,7 @@ import {loadChromSizes} from "./chromSizes.js"
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import ChromAliasDefaults from "./chromAliasDefaults.js"
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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {loadHub} from "../ucsc/hub/hubParser.js"
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import {updateReference} from "./updateReference.js"
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const ucsdIDMap = new Map([
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["1kg_ref", "hg18"],
@@ -32,6 +33,7 @@ class Genome {
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static async createGenome(options, browser) {
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updateReference(options)
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const genome = new Genome(options, browser)
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await genome.init()
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return genome

‎js/genome/updateReference.js

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/**
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* Update deprecated fasta & index urls in the reference object.
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*/
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const isString = (x) => {
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return x && typeof x === "string" || x instanceof String
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}
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/**
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* Replaces deprecated s3 fasta URLs with twoBitURLs. The purpose here is to rescue references from saved sessions
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* that contain pointers to deprectated IGV s3 buckets. These buckets will eventually be deleted
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*
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* @param reference
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*/
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function updateReference(reference) {
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if (!(requiresUpdate(reference) && updates[reference.id])) {
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return
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}
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const updatedReference = updates[reference.id]
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if (updatedReference) {
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delete reference.fastaURL
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if (reference.indexURL) delete reference.indexURL
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reference.twoBitURL = updatedReference.twoBitURL
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if (updatedReference.twoBitBptURL) reference.twoBitBptURL = updatedReference.twoBitBptURL
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if (updatedReference.chromSizesURL) reference.chromSizesURL = updatedReference.chromSizesURL
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}
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}
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function requiresUpdate(reference) {
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return isString(reference.fastaURL) &&
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(reference.fastaURL.startsWith("https://igv.org") ||
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["igv.org.genomes", "igv.broadinstitute.org", "igv.genepattern.org", "igvdata.broadinstitute.org",
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"igv-genepattern-org"].some(bucket => reference.fastaURL.includes(bucket)))
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}
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const updates = {
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"hs1": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt"
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},
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"hg38": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes"
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},
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"hg19": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes"
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},
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"hg18": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/hg18.chrom.sizes"
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},
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"mm39": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes"
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},
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"mm10": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes"
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},
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"mm9": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.chrom.sizes"
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},
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"rn7": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/227/675/GCF_015227675.2/GCF_015227675.2.chrom.sizes.txt"
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},
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"rn6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/895/GCF_000001895.5/GCF_000001895.5.chrom.sizes.txt"
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},
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"gorGor6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chrom.sizes"
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},
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"gorGor4": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/bigZips/gorGor4.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/bigZips/gorGor4.chrom.sizes"
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},
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"panTro6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chrom.sizes"
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},
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"panTro5": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips/panTro5.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips/panTro5.chrom.sizes"
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},
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"panTro4": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips/panTro4.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips/panTro4.chrom.sizes"
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},
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"macFas5": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chrom.sizes"
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},
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"panPan2": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panPan2/bigZips/panPan2.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panPan2/bigZips/panPan2.chrom.sizes"
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},
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"canFam6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chrom.sizes"
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},
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"canFam5": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chrom.sizes"
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},
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"canFam4": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.chrom.sizes"
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},
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"canFam3": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips/canFam3.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips/canFam3.chrom.sizes"
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},
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"bosTau9": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chrom.sizes"
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},
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"bosTau8": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.chrom.sizes"
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},
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"susScr11": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.chrom.sizes"
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},
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"galGal6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chrom.sizes"
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},
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"danRer11": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.chrom.sizes"
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},
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"danRer10": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.chrom.sizes"
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},
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"ce11": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.chrom.sizes"
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},
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"dm6": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chrom.sizes"
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},
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"dm3": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes"
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},
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"sacCer3": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt"
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},
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"GCF_000002945.1": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt"
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},
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"GCF_009858895.2": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.chrom.sizes.txt"
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},
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"tair10": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.2bit",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chrom.sizes.txt"
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},
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"GCA_000022165.1": {
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.2bit",
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"twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.2bit.bpt",
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"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/022/165/GCA_000022165.1/GCA_000022165.1.chrom.sizes.txt"
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}
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}
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export {updateReference}
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