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index-backup.html
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<!DOCTYPE html>
<html lang="en" class="igv-app-html">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no">
<meta name="description" content="">
<meta name="author" content="">
<meta http-equiv=“Pragma” content=”no-cache”>
<meta http-equiv=“Expires” content=”-1″>
<meta http-equiv=“CACHE-CONTROL” content=”NO-CACHE”>
<title>IGV</title>
<link rel="shortcut icon" href="favicon.ico" type="image/x-icon"/>
<!-- Font Awesome -->
<link rel="stylesheet" href="css/fontawesome/all.css">
<!-- Bootstrap 5.3 CSS -->
<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH" crossorigin="anonymous">
<!-- DataTables CSS -->
<link rel="stylesheet" href="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.css">
<!-- CSS -->
<link rel="stylesheet" href="css/app.css">
<!-- Bootstrap 5.3 JS -->
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz" crossorigin="anonymous"></script>
<!-- jQuery -->
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
<!-- Circular View -->
<script src="https://unpkg.com/[email protected]/umd/react.development.js" defer></script>
<script src="https://unpkg.com/[email protected]/umd/react-dom.development.js" defer></script>
<script src="https://unpkg.com/@jbrowse/[email protected]/dist/react-circular-genome-view.umd.production.min.js" defer></script>
<!-- Datatables JS -->
<script type="text/javascript" src="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.js"></script>
<!-- Google Platform JS -->
<script src="https://apis.google.com/js/platform.js"></script>
<!-- Google GSI -->
<script src="https://accounts.google.com/gsi/client"></script>
<script type="text/javascript" src="./igvwebConfig.js"></script>
<script type="module" src="js/app.js"></script>
<!-- CSS to hide the track select menu of the jBrowse circular view -->
<style>
button[data-testid='circular_track_select'] {
display: none;
}
</style>
</head>
<body class="igv-app-body-footerized">
<nav class="navbar fixed-top py-0 navbar-expand-sm navbar-dark">
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#igv-app-navbar-navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="igv-app-navbar-navigation" class="collapse navbar-collapse">
<ul class="navbar-nav mr-auto">
<!-- Genome -->
<li class="nav-item px-3">
<div class="dropdown">
<a id="igv-app-genome-dropdown-button" class="dropdown-toggle" href="#" data-toggle="dropdown">
Genome
</a>
<div id="igv-app-genome-dropdown-menu" class="dropdown-menu">
<!-- local file -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="igv-app-dropdown-local-genome-file-input" type="file" name="file"
multiple style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="igv-app-dropdown-dropbox-genome-file-button"
class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox</div>
<div><img id="igv-app-genome-dropbox-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- Google Drive -->
<div class="dropdown-item">
<div id="igv-app-dropdown-google-drive-genome-file-button"
class="igv-app-dropdown-item-cloud-storage">
<div>Google Drive</div>
<div><img id="igv-app-genome-google-drive-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- URL -->
<button class="dropdown-item" type="button" data-toggle="modal" data-target="#igv-app-genome-from-url-modal">
URL ...
</button>
<!-- Genark (track hubs) -->
<button class="dropdown-item" type="button" data-toggle="modal" data-target="#igv-app-genome-genark-modal">
UCSC GenArk ...
</button>
<div id="igv-app-genome-dropdown-divider" class="dropdown-divider"></div>
</div>
</div>
</li>
<!-- Tracks -->
<li class="nav-item px-3">
<div id="igv-app-track-dropdown" class="dropdown">
<a id="igv-track-dropdown-button" class="dropdown-toggle" href="#" data-toggle="dropdown">
Tracks
</a>
<div id="igv-app-track-dropdown-menu" class="dropdown-menu">
<!-- local file -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="igv-app-dropdown-local-track-file-input" type="file" name="file" multiple
style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="igv-app-dropdown-dropbox-track-file-button"
class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox</div>
<div><img id="igv-app-track-dropbox-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- Google Drive -->
<div class="dropdown-item">
<div id="igv-app-dropdown-google-drive-track-file-button"
class="igv-app-dropdown-item-cloud-storage">
<div>Google Drive</div>
<div><img id="igv-app-track-google-drive-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- URL -->
<button class="dropdown-item" type="button" data-toggle="modal"
data-target="#igv-app-track-from-url-modal">
URL ...
</button>
<div id="igv-app-annotations-section" class="dropdown-divider">
</div>
</div>
</div>
</li>
<!-- Sample Info File -->
<li class="nav-item px-3">
<div id="igv-app-sample-info-dropdown" class="dropdown">
<a id="igv-app-sample-info-dropdown-button" class="dropdown-toggle" href="#" data-toggle="dropdown">
Sample Info
</a>
<div id="igv-app-sample-info-dropdown-menu" class="dropdown-menu">
<!-- local file -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="igv-app-sample-info-dropdown-local-track-file-input" type="file" name="file" multiple style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<div class="dropdown-item">
<div id="igv-app-dropdown-dropbox-sample-info-file-button" class="igv-app-dropdown-item-cloud-storage">
<div>Dropbox</div>
<div><img id="igv-app-sample-info-dropbox-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- Google Drive -->
<div class="dropdown-item">
<div id="igv-app-dropdown-google-drive-sample-info-file-button" class="igv-app-dropdown-item-cloud-storage">
<div>Google Drive</div>
<div><img id="igv-app-sample-info-google-drive-button-image" width="18" height="18"></div>
<div>...</div>
</div>
</div>
<!-- URL -->
<button class="dropdown-item" type="button" data-toggle="modal" data-target="#igv-app-sample-info-from-url-modal">
URL ...
</button>
</div>
</div>
</li>
<!-- Session -->
<li class="nav-item px-3">
<div class="dropdown">
<a id="igv-app-session-dropdown-button" class="dropdown-toggle" href="#" data-toggle="dropdown">
Session
</a>
<div id="igv-session-dropdown-menu" class="dropdown-menu">
<!-- Load local session file -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="igv-app-dropdown-local-session-file-input" type="file" name="file"
style="display: none;">
</div>
</div>
</label>
<!-- Dropbox -->
<!-- Google Drive -->
<!-- Session URL -->
<button class="dropdown-item" type="button" data-toggle="modal"
data-target="#igv-app-session-url-modal">
Load URL ...
</button>
<div class="dropdown-divider"></div>
<!-- Save local session file -->
<button class="dropdown-item" type="button" data-toggle="modal" id="save-session-button" data-target="#igv-app-session-save-modal">
Save ...
</button>
</div>
</div>
</li>
<!-- Share (generate URL) -->
<li class="nav-item px-3">
<div>
<a id="igv-app-share-button" href="#" data-toggle="modal" data-target="#igv-app-share-modal">
Share
</a>
</div>
</li>
<!-- Bookmark -->
<li class="nav-item px-3">
<div>
<a id="igv-app-bookmark-button" href="#">
Bookmark
</a>
</div>
</li>
<!-- Save Image. SVG or PNG -->
<li class="nav-item px-3">
<div class="dropdown">
<a id="igv-app-save-image-dropdown-button" href="#" data-toggle="dropdown">
Save Image
</a>
<div id="igv-app-save-image-dropdown-menu" class="dropdown-menu">
<!-- SVG -->
<div class="dropdown-item">
<a id="igv-app-save-svg-button" href="#" data-toggle="modal" data-target="#igv-app-svg-save-modal">
Save as SVG ...
</a>
</div>
<!-- PNG -->
<div class="dropdown-item">
<a id="igv-app-save-png-button" href="#" data-toggle="modal" data-target="#igv-app-png-save-modal">
Save as PNG ...
</a>
</div>
</div>
</div>
</li>
<!-- Circular View -->
<li id="igv-app-circular-view-nav-item" class="nav-item px-3" style="display: none;">
<div id="igv-app-circular-view-dropdown" class="dropdown">
<a id="igv-app-circular-view-dropdown-button" class="dropdown-toggle" href="#"
data-toggle="dropdown">Circular View</a>
<div id="igv-app-circular-view-dropdown-menu" class="dropdown-menu">
<button id="igv-app-circular-view-presentation-button" class="dropdown-item" type="button">
Show
</button>
<button id="igv-app-circular-view-clear-chords-button" class="dropdown-item" type="button"
disabled>
Clear All
</button>
<button id="igv-app-circular-view-resize-button" class="dropdown-item" type="button" disabled
data-toggle="modal" data-target="#igv-app-circular-view-resize-modal">
Resize
</button>
<a id="igv-app-circular-view-example-button" class="dropdown-item" type="button"
href="https://github.com/igvteam/igv-webapp/wiki/Circular-View"
target="_blank">Documentation</a>
</div>
</div>
</li>
<!-- Help Menu -->
<li class="nav-item px-3">
<div id="igv-app-help-dropdown" class="dropdown">
<a id="igv-app-help-button" class="dropdown-toggle" href="#" data-toggle="dropdown">
Help
</a>
<div class="dropdown-menu">
<a class="dropdown-item" href="https://igv.org/doc/webapp/#ExampleSessions" target="_blank">Example Sessions</a>
<a class="dropdown-item" href="https://igv.org/doc/webapp/" target="_blank">Documentation</a>
<a class="dropdown-item" href="https://github.com/igvteam/igv-webapp" target="_blank">GitHub
Repository</a>
<a class="dropdown-item" href="https://groups.google.com/group/igv-help" target="_blank">User
Forum</a>
<a class="dropdown-item" href="#" data-toggle="modal" data-target="#igv-app-help-about-modal">About
IGV-Web</a>
<a class="dropdown-item" href="https://igv.org/doc/privacy.html" target="_blank">Privacy Policy</a>
</div>
</div>
</li>
</ul>
<!-- Google Authentication -->
<div class="btn-group">
<div class="btn-group dropleft" role="group">
<div id="igv-google-drive-dropdown" class="dropdown">
<button id="igv-google-drive-dropdown-toggle" type="button" class="btn dropdown-toggle" data-toggle="dropdown" style="display: none;">
<img src="img/google-drive-current.png" width="24" height="24">
</button>
<div class="dropdown-menu">
<button id="igv-google-drive-sign-out-button" class="dropdown-item" type="button">
</button>
</div>
</div>
</div>
</div>
</div>
</nav>
<main id="igv-main" role="main" class="container-fluid">
<!-- JBrowser Circular Viewer Container -->
<div id="igv-circular-view-container"
style="position: absolute; top:200px; left:20px; width: fit-content; height: fit-content;z-index: 2048"></div>
<!-- App container -->
<div class="row">
<div class="col-sm">
<div id="igv-app-container">
</div>
</div>
</div>
<!-- Share URL Modal -->
<div id="igv-app-share-modal" class="modal fade">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<div id="igv-app-share-input-modal-close-button" class="modal-title">Share</div>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<!-- copy URL section -->
<div class="modal-body-section">
<div class="container">
<!-- Copy URL radio buttons -->
<div id="igv-share-url-radio-pair-container" class="form-group">
<div class="custom-control custom-radio custom-control-inline">
<input type="radio" id="igv-share-short-url-radio" name="share-url-radio-pair" class="custom-control-input">
<label class="custom-control-label" for="igv-share-short-url-radio">Shortened URL</label>
</div>
<div class="custom-control custom-radio custom-control-inline">
<input type="radio" id="igv-share-long-url-radio" name="share-url-radio-pair" class="custom-control-input" checked>
<label class="custom-control-label" for="igv-share-long-url-radio">Long URL</label>
</div>
</div>
<!-- Copy URL -->
<div class="row no-gutters">
<div class="col mr-2">
<div class="input-group input-group-sm">
<input id="igv-app-share-input" type="text" class="form-control" placeholder="">
</div>
</div>
<div class="col-4">
<button id="igv-app-copy-link-button" class="btn btn-sm btn-outline-secondary" type="button">Copy Session URL</button>
</div>
</div>
<!-- Embed iframe Button | Copy iframe Button -->
<div class="row pt-4">
<div class="col text-center">
<div class="d-flex">
<button id="igv-app-embed-button" type="button" class="btn btn-sm btn-outline-secondary mr-2">Embeddable iframe</button>
<button id="igv-app-copy-iframe-button" type="button" class="btn btn-sm btn-outline-secondary">Copy iframe</button>
</div>
</div>
</div>
<!-- Embed -->
<div id="igv-app-embed-container" class="row">
<div class="col form-group">
<textarea class="form-control" rows="4"></textarea>
</div>
</div>
<!-- QR Code Button -->
<div id="igv-app-qrcode-container" class="row pt-4">
<div class="col">
<button id="igv-app-qrcode-button" type="button" class="btn btn-sm btn-outline-secondary">Create QR Code</button>
</div>
</div>
<!-- QR Code -->
<div class="row">
<div id="igv-app-qrcode-image" class="col">
</div>
</div>
</div>
</div>
</div>
</div>
<!-- SVG save -->
<div id="igv-app-svg-save-modal" class="modal fade igv-app-file-save-modal">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<div id="igv-app-svg-save-modal-label" class="modal-title">
<div>
Save SVG File
</div>
</div>
<button type="button" class="close" data-dismiss="modal">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<input class="form-control" type="text" placeholder="igv-app.svg">
<div>
Enter filename with .svg suffix
</div>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-sm btn-outline-secondary" data-dismiss="modal">Cancel</button>
<button type="button" class="btn btn-sm btn-secondary">OK</button>
</div>
</div>
</div>
</div>
<!-- PNG save -->
<div id="igv-app-png-save-modal" class="modal fade igv-app-file-save-modal">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<div id="igv-app-png-save-modal-label" class="modal-title">
<div>
Save PNG File
</div>
</div>
<button type="button" class="close" data-dismiss="modal">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<input class="form-control" type="text" placeholder="igv-app.png">
<div>
Enter filename with .png suffix
</div>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-sm btn-outline-secondary" data-dismiss="modal">Cancel</button>
<button type="button" class="btn btn-sm btn-secondary">OK</button>
</div>
</div>
</div>
</div>
<!-- Help - About - Modal -->
<div id="igv-app-help-about-modal" class="modal fade" tabindex="-1">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">About IGV-Web</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div id="igv-app-version"></div>
<div id="igv-igvjs-version"></div>
</div>
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<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
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</main>
<footer class="igv-app-footer">
<div>
<a href="https://igv.org" target="_blank">
<img src="img/igv-logo-cooked-40x40.png" width="32" height="32"> igv.org
</a>
</div>
<div id="igv-version-label">
</div>
<div>
<div id="igv-app-ucsd-logo">
<a href="https://ucsd.edu/" target="_blank" title="University of California at San Diego">
<img src="img/ucsd-logo.svg" width="123" height="24" alt="University of California at San Diego">
</a>
</div>
<div id="igv-app-broad-logo">
<a href="https://www.broadinstitute.org" target="_blank" title="Broad Institute home page">
<img src="https://igv.org/app/img/broad-institute-logo.svg" width="95" height="24"
alt="Broad Institute logo">
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