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Bug fix: Save Image #1888

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merged 1 commit into from
Oct 2, 2024
Merged

Bug fix: Save Image #1888

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74 changes: 74 additions & 0 deletions dev/issues/git-1886.html
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Original file line number Diff line number Diff line change
@@ -0,0 +1,74 @@
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Git Issue - 1886</title>
</head>
<body>

<header>
<h1>Git Issue - 1886</h1>
</header>

<main>
<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
</main>

<script type="module">

import igv from "../../js/index.js"

const config =
{
"version": "3.0.5",
"showSampleNames": false,
"reference": {
"id": "hg19",
"name": "Human (GRCh37/hg19)",
"fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta",
"indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg19/hg19.fasta.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chromAlias.txt",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes",
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
},
"locus": "chr3:86,924,605-86,924,924",
"roi": [],
"tracks": [
{
"type": "sequence",
"order": -9007199254740991
},
{
"sourceType": "gcs",
"type": "alignment",
"url": "gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam",
"indexURL": "gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam.bai",
"name": "NA12889",
"order": 0,
"colorBy": "unexpectedPair"
},
{
"name": "Refseq Genes",
"format": "refgene",
"id": "hg19_genes",
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz",
"indexed": false,
"order": 1000000,
"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$",
"type": "annotation",
"height": 70
}
]
}

igv.createBrowser(document.getElementById('igvDiv'), config)
.then(browser => {
console.log(`browser ${ browser.guid } is good to go`)
})

</script>
</body>
</html>
9 changes: 3 additions & 6 deletions js/bam/alignmentTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -304,6 +304,7 @@ class AlignmentTrack extends TrackBase {
if (this.groupBy && groupName) {

ctx.save()

ctx.font = '400 12px sans-serif'
const textMetrics = ctx.measureText(groupName)
const w = textMetrics.width + 10
Expand All @@ -314,14 +315,10 @@ class AlignmentTrack extends TrackBase {
ctx.textAlign = "center"
ctx.fillStyle = 'white'
ctx.strokeStyle = 'lightGray'
ctx.beginPath()
ctx.roundRect(x, baselineY - textMetrics.actualBoundingBoxAscent - 5, w, h, 2)
ctx.fill()
ctx.stroke()
IGVGraphics.roundRect(ctx, x, baselineY - textMetrics.actualBoundingBoxAscent - 5, w, h, 2, 1, 1)

ctx.fillStyle = 'black'
ctx.fillText(groupName, x + w / 2, baselineY)

IGVGraphics.dashedLine(ctx, 0, alignmentY, pixelWidth, alignmentY)

ctx.restore()
Expand Down Expand Up @@ -1229,7 +1226,7 @@ class AlignmentTrack extends TrackBase {
const y = clickState.y
const offsetY = y - this.top
const genomicLocation = clickState.genomicLocation

if(features.packedGroups) {
let minGroupY = Number.MAX_VALUE
for (let group of features.packedGroups.values()) {
Expand Down
5 changes: 4 additions & 1 deletion js/trackViewport.js
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Original file line number Diff line number Diff line change
Expand Up @@ -475,7 +475,8 @@ class TrackViewport extends Viewport {

context.saveWithTranslationAndClipRect(id, x, y, width, height, yClipOffset)

let {start, bpPerPixel} = this.referenceFrame
const {start, bpPerPixel} = this.referenceFrame
const pixelXOffset = Math.round((start - this.referenceFrame.start) / bpPerPixel)

const config =
{
Expand All @@ -486,6 +487,8 @@ class TrackViewport extends Viewport {
pixelTop: yClipOffset,
pixelWidth: width,
pixelHeight: height,
pixelXOffset,
pixelShift: pixelXOffset,
bpStart: start,
bpEnd: start + (width * bpPerPixel),
bpPerPixel,
Expand Down
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