Bug fix -- hub.txt session defaults were not set

Author: jrobinso

dev/ucsc/hub.html

@@ -35,7 +35,7 @@
 
 
     const hubOptions = {
-        url: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt",
+        url: "https://hgdownload.soe.ucsc.edu/hubs/GCA/018/471/515/GCA_018471515.1/hub.txt",
         includeTracks: "all"
     }
 
@@ -45,6 +45,7 @@
 
     const igvConfig = {
         locus: hub.getDefaultPosition(),
+        showChromosomeWidget: false,
         reference: ref
     }
 

js/browser.js

@@ -55,6 +55,7 @@ import Hub from "./ucsc/ucscHub.js"
 import MultiTrackSelectButton from "./ui/multiTrackSelectButton.js"
 import MenuUtils from "./ui/menuUtils.js"
 import Genome from "./genome/genome.js"
+import {setDefaults} from "./igv-create.js"
 
 // css - $igv-scrollbar-outer-width: 14px;
 const igv_scrollbar_outer_width = 14
@@ -454,6 +455,9 @@ class Browser {
      */
     async loadSession(options) {
 
+        // UCSC hub hack
+        const chromosomeSelectWidget = this.chromosomeSelectWidget
+
         this.sampleInfo.initialize()
 
         // TODO: deprecated
@@ -490,13 +494,17 @@ class Browser {
 
                 } else if (filename.endsWith("hub.txt")) {
                     const hub = await Hub.loadHub(options)
+                    if(chromosomeSelectWidget) {
+                        chromosomeSelectWidget.hide()
+                    }
                     const genomeConfig = hub.getGenomeConfig(options.includeTracks)
                     const initialLocus = hub.getDefaultPosition()
-                    return {
+                    const config = {
                         showChromosomeWidget: false,
                         locus: initialLocus,
                         reference: genomeConfig
                     }
+                    return setDefaults(config)
                 } else if (filename.endsWith(".json")) {
                     return igvxhr.loadJson(urlOrFile)
                 } else {
@@ -516,6 +524,7 @@ class Browser {
 
         // prepare to load a new session, discarding DOM and state
         this.cleanHouseForSession()
+        this.config = session
 
         // Check for juicebox session
         if (session.browsers) {

js/genome/genome.js

@@ -143,19 +143,21 @@ class Genome {
 
     async loadChromosome(chr) {
 
-        if (this.chromAlias) {   // Try alias
-            const chromAliasRecord = await this.chromAlias.search(chr)
-            if (chromAliasRecord) {
-                chr = chromAliasRecord.chr
-            }
-        }
-
         if (!this.chromosomes.has(chr)) {
             const sequenceRecord = await this.sequence.getSequenceRecord(chr)
             if (sequenceRecord) {
                 const chromosome = new Chromosome(chr, 0, sequenceRecord.bpLength)
                 this.chromosomes.set(chr, chromosome)
             } else {
+                // Try alias
+                if (this.chromAlias) {
+                    const chromAliasRecord = await this.chromAlias.search(chr)
+                    if (chromAliasRecord) {
+                        const chromosome = new Chromosome(chromAliasRecord.chr, 0, sequenceRecord.bpLength)
+                        this.chromosomes.set(chr, chromosome)
+                    }
+                }
+
                 this.chromosomes.set(chr, undefined)  // Prevents future attempts
             }
         }

js/igv-create.js

@@ -199,6 +199,8 @@ function setDefaults(config) {
         config.tracks = []
     }
 
+    return config
+
 }
 
 
@@ -282,4 +284,4 @@ async function createTrack(config, browser) {
     return await Browser.prototype.createTrack.call(browser, config)
 }
 
-export {createTrack, createBrowser, removeBrowser, removeAllBrowsers, getAllBrowsers, visibilityChange}
+export {createTrack, createBrowser, removeBrowser, removeAllBrowsers, getAllBrowsers, visibilityChange, setDefaults}

js/referenceFrame.js

@@ -129,9 +129,9 @@ class ReferenceFrame {
         const centerBP = undefined === centerBPOrUndefined ? (this.start + this.toBP(viewportWidth / 2.0)) : centerBPOrUndefined
 
         // save initial start and bpp
-        const {start, bpPerPixel} = this.start
-
-        const {bpLength} = this.getChromosome()
+        const initialStart = this.start
+        const initialBpPerPixel = this.bpPerPixel
+        const bpLength = this.getChromosome().bpLength
         const bppThreshold = scaleFactor < 1.0 ? browser.minimumBases() / viewportWidth : bpLength / viewportWidth
 
         // update bpp
@@ -148,7 +148,7 @@ class ReferenceFrame {
 
         this.end = this.start + widthBP
 
-        const viewChanged = start !== this.start || bpPerPixel !== this.bpPerPixel
+        const viewChanged = initialStart !== this.start || initialBpPerPixel !== this.bpPerPixel
         if (viewChanged) {
             await browser.updateViews(true)
         }

js/ucsc/ucscHub.js

@@ -31,10 +31,8 @@ class Hub {
     }
 
     static supportedTypes = new Set(["bigBed", "bigWig", "bigGenePred"])
-    static filterTracks = new Set(["cytoBandIdeo"])
-
-    //["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
-    //         "cpgIslandExtUnmasked", "windowMasker"])
+    static filterTracks = new Set(["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
+        "cpgIslandExtUnmasked", "windowMasker"])
 
     constructor(url, stanzas, groups) {
 
@@ -128,9 +126,10 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
         if (this.genomeStanza.hasProperty("twoBitBptUrl")) {
             config.twoBitBptURL = this.baseURL + this.genomeStanza.getProperty("twoBitBptUrl")
         }
-        if (this.genomeStanza.hasProperty("chromSizes")) {
-            config.chromSizes = this.baseURL + this.genomeStanza.getProperty("chromSizes")
-        }
+        // chromSizes can take a very long time to load, and is not useful with the default WGV = off
+        // if (this.genomeStanza.hasProperty("chromSizes")) {
+        //     config.chromSizes = this.baseURL + this.genomeStanza.getProperty("chromSizes")
+        // }
         if (this.genomeStanza.hasProperty("description")) {
             config.description += `\n${this.genomeStanza.getProperty("description")}`
         }
@@ -370,7 +369,7 @@ async function loadStanzas(options) {
             startNewNode = true
         } else {
             const key = line.substring(indent, i)
-            if(key.startsWith("#")) continue
+            if (key.startsWith("#")) continue
             const value = line.substring(i + 1)
             if (startNewNode) {
                 // Start a new node -- indent is currently ignored as igv.js does not support sub-tracks,