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jigv-template.html
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jigv-template.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="Brent Pedersen" />
<meta name="author" content="Joe Brown" />
<title>jigv - easy self-contained igv.js reports</title>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.4.1/js/bootstrap.bundle.min.js"></script>
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Patrick+Hand&display=swap">
<link rel="stylesheet" type="text/css"
href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.4.1/css/bootstrap.min.css">
<style>
.navbar-brand {
font-family: 'Patrick Hand', cursive;
font-size: 1.5rem;
}
div.tooltip-inner {
max-width: 350px;
}
.igv-nav-bar-left-container svg {
vertical-align: top !important;
}
.igv-popover-header svg {
vertical-align: top !important;
}
.igv-logo {
margin-top: 0px !important;
}
.popover-label {
font-weight: 600;
font-size: 1.1em;
text-transform: uppercase;
padding-left: 3px;
}
.popover-value {
/* overflow: hidden will make space for scrollbar */
overflow: visible;
white-space: nowrap;
text-overflow: ellipsis;
max-width: 256px;
display: inline-block;
}
.igv-track-label {
max-width: 300px;
}
</style>
</head>
<body>
<nav class="navbar navbar-expand-md navbar-dark bg-dark py-0">
<div class="navbar-collapse collapse w-100 order-1 order-md-0 split-collapse">
<div class="navbar-nav mr-auto">
<div class="input-group input-group-sm d-none" id="vcf-features">
<div class="input-group-prepend">
<label class="input-group-text" for="features-button-group">VCF Features</label>
</div>
<div class="input-group-append" id="features-button-group">
<button class="btn btn-secondary" id="previous-feature" type="button" data-toggle="tooltip"
title="Return to previous feature (←)">Previous</button>
<button class="btn btn-secondary" id="next-feature" type="button" data-toggle="tooltip"
title="Advance to next feature (→)">Next</button>
</div>
</div>
</div>
</div>
<div class="mx-auto-md order-0">
<button class="navbar-toggler mr-2" type="button" data-toggle="collapse" data-target=".split-collapse">
<span class="navbar-toggler-icon"></span>
</button>
<a class="navbar-brand mx-auto py-0" href="#">JIGV</a>
</div>
<div class="navbar-collapse collapse w-100 order-3 split-collapse">
<ul class="navbar-nav ml-auto">
<li class="nav-item">
<!-- preferably this would be docs -->
<a class="nav-link" href="https://github.com/brentp/jigv" target="_blank">Repo</a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/brentp/jigv/issues" target="_blank">Issues</a>
</li>
<li class="nav-item nav-link">|</li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/igvteam/igv.js"
target="_blank">igv.js</a>
</li>
</ul>
</div>
</nav>
<div class="container-fluid">
<div class="row">
<div class="col" id="jigv"></div>
</div>
</div>
<script type="text/javascript">
let meta_options = <OPTIONS>
let cache = []
let browser
$("#previous-feature").click(function () {
var e = jQuery.Event("keydown")
e.which = 37
$(document).trigger(e)
})
$("#next-feature").click(function () {
var e = jQuery.Event("keydown")
e.which = 39
$(document).trigger(e)
})
// arrow presses for feature advance
jQuery(document).on("keydown", function (e) {
// console.log("jigv")
var direction = "";
if (e.which == 39) {
direction = "right"
} else if (e.which == 37) {
direction = "left"
}
if (direction == "") {
return
}
meta_options.index += direction == "left" ? -1 : 1
meta_options.index = Math.max(0, meta_options.index)
meta_options.index = Math.min(meta_options.sessions.length -1, meta_options.index)
browser.loadSession({url: meta_options.sessions[meta_options.index]})
})
jQuery(document).ready(() => {
// register tooltips
jQuery('[data-toggle="tooltip"]').tooltip()
let div = document.getElementById("jigv")
if(meta_options.sessions.length > 1) {
jQuery('#vcf-features').removeClass('d-none')
}
// this is replaced and filled with any custom javascript from the user.
<JIGV_CUSTOM_JS>
// try to get location from url hash.
var loc = location.hash.replace(/,/g, "").substring(1)
meta_options.index = meta_options.loc2idx[loc] || 0;
meta_options["sessionURL"] = meta_options.sessions[meta_options.index];
igv.createBrowser(div, meta_options).then(function (b) {
browser = b;
browser.on('locuschange', function (referenceFrame) {
location.hash = referenceFrame.label
})
browser.on("trackclick", trackclick)
})
})
function trackclick(track, data) {
// reformat read metadata when user clicks track
if (track.type != "alignment" || !data) {
return
}
var d = { tags: [] }
var hr = 0
var done = false;
// data has the read and it's mate. the one with "Read Base:" is the
// one that we clicked on. need to count <hr> and reset.
data.forEach(function (kv) {
if(done){ return; }
if (!kv.name) {
if(kv.startsWith("--------")){
if(d["Read Base:"]) { done=true; return; }
hr = 0;
d.tags = []
return
} else {
hr += 1; return
}
}
if (hr == 3) {
d.tags.push(`${kv.name}:${kv.value}`)
} else {
if (kv.name == "Mapped") { return }
if (kv.value == "No") { return }
d[kv.name] = kv.value
}
})
if (!d["Read Name"]) return; // the coverage track is also type alignment
var html = `
<table class="igv-popover-table">
<tr><td>${d["Read Name"]}</td></tr>
<tr>
<td><span class="popover-label">read:</span> ${d["Alignment Start"]} ${d["Read Strand"]}
<span class="popover-label">cigar:</span> ${d["Cigar"]}
<span class="popover-label">mapQ:</span> ${d["Mapping Quality"]}</td>
</tr>
`
if (d["Pair Orientation"]) {
html += `
<tr><td><span class="popover-label">mate-position:</span> ${d["Mate Chromosome"]}:${d["Mate Start"]}${d["Mate Strand"]}</td></tr>
<tr>
<td><span class="popover-label">orientation:</span> ${d["Pair Orientation"]}
<span class="popover-label">insert-size:</span> ${d["Insert Size"]}</td>
</tr>
`
}
var c = {"A": "green", "C": "blue", "G": "rgb(209,113,5)", "T": "red", "N": "gray"}[(d["Read Base:"] || "N").toUpperCase()]
html += `
<tr><td><span class="popover-label">tags:</span> <span class="popover-value">${d.tags.join(" | ")}</span></td></tr>
<tr>
<td><span class="popover-label">base:</span> ${d["Genomic Location: "]} <span style="font-weight:900;color:${c}">${d["Read Base:"] || ""}</span>
<span class="popover-label">quality:</span> ${d["Base Quality:"] || ""}</td>
</tr>
</table>
`
console.log(track)
console.log(data)
console.log(d)
return html
}
</script>
</body>
</html>