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file_requirement.js
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import { commonCss } from './lib/iobio-charts/common.js';
const Template = document.createElement('template');
Template.innerHTML = `
<style>
${commonCss}
#main {
margin: 50px auto 0;
max-width: 900px;
width: 100%;
padding: 0 15px;
box-sizing: border-box;
}
#main header {
font-family: Quicksand;
font-size: 46px;
}
#main h1, h2, h3, h4 {
font-family: Muli;
}
#main h1 {
font-size: 26px;
font-weight: normal;
}
#main h2 {
font-size: 24px;
}
#main h3 {
font-size: 18px;
margin-top: 40px;
}
#main h4 {
margin-bottom: 5px;
}
#main body {
font-family: Open Sans;
width: 900px;
font-weight: 300;
}
a {
color: var(--data-color);
text-decoration: none; !important;
}
pre {
border: none;
background: none;
}
</style>
<div id="main">
<body>
<header><a href="http://bam.iobio.io">bam<span style="color:rgb(200,200,200)">.iobio.io</span><span color> </span></a></header>
<h1>The indexed BAM</h1>
<p>bam.iobio needs indexed bam files so that it can sample regions from the entire file. Follow the instructions below to index your bam file and use bam.iobio.</p>
<h3>Install Bamtools</h3>
<p>Download and install bamtools using the instructions <a href="https://github.com/pezmaster31/bamtools/wiki/Building-and-installing">here</a>.</p>
<h3>Indexing your BAM</h3>
<p>Once you have successfully compiled bamtools, you can index your bam files with the following command:</p>
<pre>
$ /path/to/bamtools index -in mybam.bam
</pre>
<p>This command will create a new file, the index file (.bam.bai). Now you are ready to run <a href="../../../../index.html">bam.iobio</a>, selecting this file and your bam file when prompted.</p>
</body>
</div>
`;
class FileRequirement extends HTMLElement {
constructor() {
super();
this.attachShadow({ mode: 'open' });
this.shadowRoot.appendChild(Template.content.cloneNode(true));
}
}
customElements.define('iobio-file-requirements-page', FileRequirement);
export { FileRequirement }