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jrobinsojrobinso
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Hubs 2 (#1720)
Optimizations and bug fixes to support track hubs
1 parent 08e62c7 commit fe33399

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‎dev/annotation/annotation.html

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@@ -37,6 +37,14 @@ <h1>Annotation tracks</h1>
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"supportsWholeGenome": true,
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"name": "Bed - No Index"
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},
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{
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"type": "annotation",
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"format": "bigBed",
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"url": "../../genes.bb",
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"indexed": false,
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"supportsWholeGenome": true,
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"name": "Bed - No Index"
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},
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{
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"type": "annotation",
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"format": "bed",

‎dev/twobit/twobit.html

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reference: {
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id: "GCF_016699485.2",
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format: "2bit",
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twobitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
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twoBitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
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aliasBbURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chromAlias.bb",
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nameSet: "ucsc",
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wholeGenomeView: false

‎dev/twobit/twobit_aliasBB.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<title>twobit</title>
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</head>
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<body>
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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"
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const config =
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{
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showChromosomeWidget: false,
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locus: "NC_007194.1:1639659-1649659",
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reference: {
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id: "GCF_000002655.1",
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format: "2bit",
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twoBitURL: "../../test/data/twobit/GCF_000002655.1.2bit",
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chromAliasBbURL: "../../test/data/twobit/GCF_000002655.1.chromAlias.bb",
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wholeGenomeView: false,
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nameSet: 'ucsc'
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},
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tracks: [
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{
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name: "GC Percent",
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autoScale: false,
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height: 36,
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color: "rgb(0,0,0)",
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altColor: "rgb(128,128,128)",
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min: 30,
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max: 70,
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format: "bigWig",
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url: "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/bbi/GCF_000002655.1_ASM265v1.gc5Base.bw"
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}
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]
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}
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igv.createBrowser(document.getElementById('igvDiv'), config)
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.then(browser => {
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})
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</script>
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</body>
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</html>

‎dev/twobit/twobit_basic.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<title>twobit</title>
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</head>
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<body>
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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"
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const config =
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{
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showChromosomeWidget: false,
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locus: "NC_007194.1:1639659-1649659",
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reference: {
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id: "GCF_000002655.1",
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format: "2bit",
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twoBitURL: "../../test/data/twobit/GCF_000002655.1.2bit",
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wholeGenomeView: false
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},
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// tracks: [
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// {
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// name: "GC Percent",
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// autoScale: false,
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// height: 36,
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// color: "rgb(0,0,0)",
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// altColor: "rgb(128,128,128)",
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// min: 30,
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// max: 70,
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// format: "bigWig",
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// url: "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/bbi/GCF_000002655.1_ASM265v1.gc5Base.bw"
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// }
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//]
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}
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igv.createBrowser(document.getElementById('igvDiv'), config)
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.then(browser => {
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})
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</script>
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</body>
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</html>

‎dev/twobit/twobit_chromSizes.html

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reference: {
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id: "GCF_016699485.2",
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format: "2bit",
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twobitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
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twoBitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
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chromeSizes: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt",
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wholeGenomeView: false
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}

‎dev/twobit/twobit_t2t.html

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

‎dev/twobit/twobithg38.html

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"cytobandURL": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz",
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"aliasURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/hg38_alias.tab",
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"format": "2bit",
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"twobitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
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"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
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"aliasBbURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromAlias.bb",
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"tracks": [
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{

‎dev/ucsc/hub.html

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

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const hub = await Hub.loadHub(hubOptions)
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const ref = hub.getGenomeConfig()
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const igvConfig = {
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showChromosomeWidget: false,
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locus: hub.getDefaultPosition(),
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reference: ref
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reference: hub.getGenomeConfig()
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}
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const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
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//igvConfig.reference.chromAliasBbURL = undefined // TODO <- chromAliasBB is slowish
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const selector = document.getElementById("select")
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selector.addEventListener("change", () => document.getElementById("hub-input").value = selector.value)
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document.getElementById("load-genome").addEventListener("click", () =>
37-
browser.loadGenome({url: document.getElementById("hub-input").value}))
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document.getElementById("load-session").addEventListener("click", () =>
39-
browser.loadSession({url: document.getElementById("hub-input").value}))
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const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
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</script>

‎dev/wig/bigWigs.html

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

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