Hubs 2 (#1720)

Optimizations and bug fixes to support track hubs
igvteam · Oct 23, 2023 · 7c4c190 · 7c4c190
1 parent c6ce255
commit 7c4c190
Show file tree

Hide file tree

Showing 66 changed files with 4,774 additions and 867 deletions.
diff --git a/dev/annotation/annotation.html b/dev/annotation/annotation.html
@@ -37,6 +37,14 @@ <h1>Annotation tracks</h1>
                         "supportsWholeGenome": true,
                         "name": "Bed - No Index"
                     },
+                    {
+                        "type": "annotation",
+                        "format": "bigBed",
+                        "url": "../../genes.bb",
+                        "indexed": false,
+                        "supportsWholeGenome": true,
+                        "name": "Bed - No Index"
+                    },
                     {
                         "type": "annotation",
                         "format": "bed",

diff --git a/dev/twobit/twobit.html b/dev/twobit/twobit.html
@@ -18,7 +18,7 @@
             reference: {
                 id: "GCF_016699485.2",
                 format: "2bit",
-                twobitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
+                twoBitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
                 aliasBbURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chromAlias.bb",
                 nameSet: "ucsc",
                 wholeGenomeView: false

diff --git a/dev/twobit/twobit_aliasBB.html b/dev/twobit/twobit_aliasBB.html
@@ -0,0 +1,52 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>twobit</title>
+</head>
+
+<body>
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+
+    const config =
+        {
+            showChromosomeWidget: false,
+            locus: "NC_007194.1:1639659-1649659",
+            reference: {
+                id: "GCF_000002655.1",
+                format: "2bit",
+                twoBitURL: "../../test/data/twobit/GCF_000002655.1.2bit",
+                chromAliasBbURL: "../../test/data/twobit/GCF_000002655.1.chromAlias.bb",
+                wholeGenomeView: false,
+                nameSet: 'ucsc'
+            },
+            tracks: [
+                {
+                    name: "GC Percent",
+                    autoScale: false,
+                    height: 36,
+                    color: "rgb(0,0,0)",
+                    altColor: "rgb(128,128,128)",
+                    min: 30,
+                    max: 70,
+                    format: "bigWig",
+                    url: "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/bbi/GCF_000002655.1_ASM265v1.gc5Base.bw"
+                }
+            ]
+        }
+
+    igv.createBrowser(document.getElementById('igvDiv'), config)
+        .then(browser => {
+
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/dev/twobit/twobit_basic.html b/dev/twobit/twobit_basic.html
@@ -0,0 +1,50 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>twobit</title>
+</head>
+
+<body>
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+
+    const config =
+        {
+            showChromosomeWidget: false,
+            locus: "NC_007194.1:1639659-1649659",
+            reference: {
+                id: "GCF_000002655.1",
+                format: "2bit",
+                twoBitURL: "../../test/data/twobit/GCF_000002655.1.2bit",
+                wholeGenomeView: false
+            },
+            // tracks: [
+            //     {
+            //         name: "GC Percent",
+            //         autoScale: false,
+            //         height: 36,
+            //         color: "rgb(0,0,0)",
+            //         altColor: "rgb(128,128,128)",
+            //         min: 30,
+            //         max: 70,
+            //         format: "bigWig",
+            //         url: "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/bbi/GCF_000002655.1_ASM265v1.gc5Base.bw"
+            //     }
+            //]
+        }
+
+    igv.createBrowser(document.getElementById('igvDiv'), config)
+        .then(browser => {
+
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/dev/twobit/twobit_chromSizes.html b/dev/twobit/twobit_chromSizes.html
@@ -18,7 +18,7 @@
             reference: {
                 id: "GCF_016699485.2",
                 format: "2bit",
-                twobitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
+                twoBitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
                 chromeSizes: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt",
                 wholeGenomeView: false
             }

diff --git a/dev/twobit/twobit_t2t.html b/dev/twobit/twobit_t2t.html
@@ -14,60 +14,69 @@
 
     const config =
         {
-            locus: "myc",
+            //locus: "myc",
+            locus:"CP068269.2:35,726,976-35,734,192",
+            showChromosomeWidget: false,
             reference: {
-                "id": "chm13v2.0",
-                "name": "Human (T2T CHM13-v2.0)",
-                "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa",
-                "indexURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa.fai",
-                "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/CHM13_v2.0.cytoBandMapped.bed",
-                "aliasURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/GCA_009914755.4.chromAlias.txt",
-                twobitURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit",
+                wholeGenomeView: false,
+                id: "chm13v2.0",
+                name: "Human (T2T CHM13-v2.0)",
+                twoBitURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit",
                 cytobandBbURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.cytoBandMapped/cytoBandMapped.bb",
-                aliasBbURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.bb",
+                chromAliasBbURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.bb",
                 nameSet: "ucsc",
-                "tracks": [
+                tracks: [
+                    // {
+                    //     "id": "catLiftOffGenesV1",
+                    //     "name": "CAT/Liftoff Genes",
+                    //     "format": "bigbed",
+                    //     "description": " <a target = \"_blank\" href = \"https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/html/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html\">CAT + Liftoff Gene Annotations</a>",
+                    //     "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1/catLiftOffGenesV1.bb",
+                    //     "displayMode": "EXPANDED",
+                    //     "height": 200,
+                    //     "visibilityWindow": -1,
+                    //     "supportsWholeGenome": false
+                    // },
+                    //
+                    // // Include a hg38 bigwig track -- test chromosome aliasing
+                    // {
+                    //     "url": "https://www.encodeproject.org/files/ENCFF754TJH/@@download/ENCFF754TJH.bigWig",
+                    //     "name": "Encode bigwig",
+                    // },
+
+                    // plain wig track
+                    {
+                        url: "../../test/data/hubs/ENCFF754TJH.wig",
+                        name: "Encode wig"
+                    },
+
+                    // plain bed track
                     {
-                        "id": "catLiftOffGenesV1",
-                        "name": "CAT/Liftoff Genes",
-                        "format": "bigbed",
-                        "description": " <a target = \"_blank\" href = \"https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/html/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html\">CAT + Liftoff Gene Annotations</a>",
-                        "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1/catLiftOffGenesV1.bb",
-                        "displayMode": "EXPANDED",
-                        "height": 200,
-                        "visibilityWindow": -1,
-                        "supportsWholeGenome": false,
-                        "order": 1000000
+                        url: "../../test/data/hubs/catLiftOff.bed",
+                        name: "plain bed"
                     },
+
+                    // indexed bed track
                     {
-                        "id": "augustus",
-                        "name": "Augustus",
-                        "format": "bigbed",
-                        "description": " <a target = \"_blank\" href = \"https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/html/GCA_009914755.4_T2T-CHM13v2.0.augustus\">Augustus Gene Predictions</a>",
-                        "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.augustus.bb",
-                        "displayMode": "EXPANDED",
-                        "color": "180,0,0",
-                        "height": 200,
-                        "visibilityWindow": -1,
-                        "supportsWholeGenome": false,
-                        "order": 1000001
+                        url: "../../test/data/hubs/catLiftOff.bed.gz",
+                        indexUrl: "../../test/data/hubs/catLiftOff.bed.gz.tbi",
+                        name: "indexed bed"
                     },
+
+                    //bam
                     {
-                        "name": "Genes",
-                        "format": "bed",
-                        "url": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0_geneLocations.short.bed.gz",
-                        "hidden" : true,
-                        "searchable": true
+                        type: "alignment",
+                        url: "https://1000genomes.s3.amazonaws.com/phase3/data/NA19625/exome_alignment/NA19625.mapped.ILLUMINA.bwa.ASW.exome.20120522.bam",
+                        indexURL: "https://1000genomes.s3.amazonaws.com/phase3/data/NA19625/exome_alignment/NA19625.mapped.ILLUMINA.bwa.ASW.exome.20120522.bam.bai",
+                        name: "NA12878n"
                     }
                 ]
             }
 
         }
 
-    igv.createBrowser(document.getElementById('igvDiv'), config)
-        .then(browser => {
+    const browser = await igv.createBrowser(document.getElementById('igvDiv'), config)
 
-        })
 
 
 </script>

diff --git a/dev/twobit/twobithg38.html b/dev/twobit/twobithg38.html
@@ -24,7 +24,7 @@
                 "cytobandURL": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz",
                 "aliasURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/hg38_alias.tab",
                 "format": "2bit",
-                "twobitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
+                "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
                 "aliasBbURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromAlias.bb",
                 "tracks": [
                     {

diff --git a/dev/ucsc/hub.html b/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
     }
 

diff --git a/dev/ucsc/slowHub.html b/dev/ucsc/slowHub.html
@@ -22,21 +22,16 @@
 
 
     const hub = await Hub.loadHub(hubOptions)
-    const ref = hub.getGenomeConfig()
 
     const igvConfig = {
+        showChromosomeWidget: false,
         locus: hub.getDefaultPosition(),
-        reference: ref
+        reference: hub.getGenomeConfig()
     }
 
-    const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
+    //igvConfig.reference.chromAliasBbURL = undefined   // TODO <- chromAliasBB is slowish
 
-    const selector = document.getElementById("select")
-    selector.addEventListener("change", () => document.getElementById("hub-input").value = selector.value)
-    document.getElementById("load-genome").addEventListener("click", () =>
-        browser.loadGenome({url: document.getElementById("hub-input").value}))
-    document.getElementById("load-session").addEventListener("click", () =>
-        browser.loadSession({url: document.getElementById("hub-input").value}))
+    const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
 
 
 </script>

diff --git a/dev/wig/bigWigs.html b/dev/wig/bigWigs.html
@@ -29,17 +29,17 @@
                     "Bar": 999.999
                 }
             },
-            {
-                "url": "https://www.encodeproject.org/files/ENCFF754TJH/@@download/ENCFF754TJH.bigWig",
-                "graphType": "points",
-                "pointSize": 3,
-                "name": "Encode bigwig points"
-            },
-            {
-                "url": "https://www.encodeproject.org/files/ENCFF754TJH/@@download/ENCFF754TJH.bigWig",
-                "graphType": "line",
-                "name": "Encode bigwig line"
-            },
+            // {
+            //     "url": "https://www.encodeproject.org/files/ENCFF754TJH/@@download/ENCFF754TJH.bigWig",
+            //     "graphType": "points",
+            //     "pointSize": 3,
+            //     "name": "Encode bigwig points"
+            // },
+            // {
+            //     "url": "https://www.encodeproject.org/files/ENCFF754TJH/@@download/ENCFF754TJH.bigWig",
+            //     "graphType": "line",
+            //     "name": "Encode bigwig line"
+            // },
             {
                 "url": "https://s3-us-west-2.amazonaws.com/ilmn.igv-test/test2.bigWig",
                 color: 'rgb(0,0,255)',