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Hubs 2 #1720

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merged 14 commits into from
Oct 23, 2023
Merged

Hubs 2 #1720

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1cf90c8
Revert "Auxiliary commit to revert individual files from 67cf4f34cef9…
jrobinso Oct 6, 2023
f50f42c
.
jrobinso Oct 10, 2023
cbd8893
Bigwig and sequence track working with aliases
jrobinso Oct 13, 2023
c5d2d9c
Use specified name set (e.g. UCSC) for chromosome display name
jrobinso Oct 15, 2023
b6198d0
.
jrobinso Oct 19, 2023
2b418af
Use indexes wherever possible
jrobinso Oct 19, 2023
d226689
Use indexes wherever possible ...
jrobinso Oct 19, 2023
ed7601e
rebase (#1718)
jrobinso Oct 20, 2023
fbac466
.
jrobinso Oct 20, 2023
babdedf
.
jrobinso Oct 20, 2023
b8cda23
.
jrobinso Oct 21, 2023
c7444ee
fix unit tests
jrobinso Oct 22, 2023
4486c57
Bug fix -- hub.txt session defaults were not set
jrobinso Oct 23, 2023
25ef60b
Merge branch 'master' into hubs_2
jrobinso Oct 23, 2023
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8 changes: 8 additions & 0 deletions dev/annotation/annotation.html
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Expand Up @@ -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",
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2 changes: 1 addition & 1 deletion dev/twobit/twobit.html
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Expand Up @@ -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
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52 changes: 52 additions & 0 deletions dev/twobit/twobit_aliasBB.html
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@@ -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>
50 changes: 50 additions & 0 deletions dev/twobit/twobit_basic.html
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@@ -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>
2 changes: 1 addition & 1 deletion dev/twobit/twobit_chromSizes.html
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Expand Up @@ -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
}
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87 changes: 48 additions & 39 deletions dev/twobit/twobit_t2t.html
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion dev/twobit/twobithg38.html
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Expand Up @@ -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": [
{
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3 changes: 2 additions & 1 deletion dev/ucsc/hub.html
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Expand Up @@ -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"
}

Expand All @@ -45,6 +45,7 @@

const igvConfig = {
locus: hub.getDefaultPosition(),
showChromosomeWidget: false,
reference: ref
}

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13 changes: 4 additions & 9 deletions dev/ucsc/slowHub.html
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Expand Up @@ -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>
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22 changes: 11 additions & 11 deletions dev/wig/bigWigs.html
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Expand Up @@ -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)',
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