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test38.html
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<!DOCTYPE html>
<html>
<head>
<style>
</style>
<title>Human GRCh38 :: Dalliance</title>
<script language="javascript" src="node_modules/es6-promise/dist/promise-0.1.2.js"></script>
<script language="javascript" src="js/bam.js"></script>
<script language="javascript" src="js/bigwig.js"></script>
<script language="javascript" src="js/das.js"></script>
<script language="javascript" src="js/spans.js"></script>
<script language="javascript" src="js/utils.js"></script>
<script language="javascript" src="js/cbrowser.js"></script>
<script language="javascript" src="js/feature-popup.js"></script>
<script language="javascript" src="js/tier.js"></script>
<script language="javascript" src="js/features.js"></script>
<script language="javascript" src="js/color.js"></script>
<script language="javascript" src="js/feature-draw.js"></script>
<script language="javascript" src="js/sequence-draw.js"></script>
<script language="javascript" src="js/domui.js"></script>
<script language="javascript" src="js/track-adder.js"></script>
<script language="javascript" src="js/chainset.js"></script>
<script language="javascript" src="js/version.js"></script>
<script language="javascript" src="js/sha1.js"></script>
<script language="javascript" src="js/sample.js"></script>
<script language="javascript" src="js/kspace.js"></script>
<script language="javascript" src="js/bin.js"></script>
<script language="javascript" src="js/twoBit.js"></script>
<script language="javascript" src="js/thub.js"></script>
<script language="javascript" src="js/svg-export.js"></script>
<script language="javascript" src="node_modules/jszlib/js/inflate.js"></script>
<script language="javascript" src="js/browser-ui.js"></script>
<script language="javascript" src="js/glyphs.js"></script>
<script language="javascript" src="js/session.js"></script>
<script language="javascript" src="js/jbjson.js"></script>
<script language="javascript" src="js/sourceadapters.js"></script>
<script language="javascript" src="polyfills/html5slider.js"></script>
<script language="javascript" src="js/ensembljson.js"></script>
<script language="javascript" src="js/overlay.js"></script>
<script language="javascript" src="js/tier-actions.js"></script>
<script language="javascript" src="js/tier-edit.js"></script>
<script language="javascript" src="js/search.js"></script>
<script language="javascript" src="js/tabix.js"></script>
<script language="javascript" src="js/tabix-source.js"></script>
<script language="javascript" src="js/bigtab.js"></script>
<script language="javascript" src="js/memstore.js"></script>
<script language="javascript" src="js/vcf.js"></script>
<script language="javascript" src="js/bedwig.js"></script>
<script language="javascript" src="js/probe.js"></script>
<script language="javascript" src="js/trix.js"></script>
<script language="javascript" src="js/export-ui.js"></script>
<script language="javascript" src="js/export-config.js"></script>
<script language="javascript" src="js/export-image.js"></script>
<script language="javascript" src="js/lh3utils.js"></script>
<script language="javascript" src="js/svg-utils.js"></script>
<script language="javascript" src="js/numformats.js"></script>
<script language="javascript" src="js/cigar.js"></script>
<script language="javascript" src="js/style.js"></script>
<script language="javascript">
var b = new Browser({
chr: '22',
viewStart: 30000000,
viewEnd: 30030000,
cookieKey: 'human-grc_h38-test',
coordSystem: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: '38',
ucscName: 'hg38',
},
chains: {
hg19ToHg38: {uri: 'http://www.derkholm.net:8080/das/hg19ToHg38/',
srcTag: 'GRCh37',
destTag: 'GRCh38',
coords: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: 37
}
}
},
sources: [{name: 'Genome',
twoBitURI: 'http://www.biodalliance.org/datasets/hg38.2bit',
tier_type: 'sequence',
provides_entrypoints: true,
pinned: true
},
{name: 'GENCODE',
bwgURI: 'http://www.biodalliance.org/datasets/gencode/gencode.v20.annotation.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode2.xml',
collapseSuperGroups: true,
trixURI: 'http://www.biodalliance.org/datasets/gencode/gencode.v20.annotation.ix'},
{name: 'GENCODEv19',
bwgURI: 'http://www.biodalliance.org/datasets/gencode/gencode.v19.annotation.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode2.xml',
collapseSuperGroups: true,
trixURI: 'http://www.biodalliance.org/datasets/gencode/gencode.v19.annotation.ix',
mapping: 'hg19ToHg38'},
{name: 'Repeats',
desc: 'Repeat annotation from RepeatMasker',
bwgURI: 'http://www.biodalliance.org/datasets/GRCh38/repeats.bb',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats2.xml',
forceReduction: -1},
{name: 'SNPs',
tier_type: 'ensembl',
species:'human',
type: 'variation',
disabled: true,
featureInfoPlugin: function(f, info) {
if (f.id) {
info.add('SNP', makeElement('a', f.id, {href: 'http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=' + f.id, target: '_newtab'}));
}
}
}
],
setDocumentTitle: true,
prefix: '',
fullScreen: true,
});
b.hubs = [
'http://www.biodalliance.org/datasets/testhub/hub.txt',
'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt'
];
b.addFeatureInfoPlugin(function(f, info) {
info.add('Testing', 'This is a test!');
});
b.addViewListener(function(chr, min, max) {
var link = document.getElementById('enslink');
link.href = 'http://www.ensembl.org/Homo_sapiens/Location/View?r=' + chr + ':' + min + '-' + max;
});
var geneDescriptions;
connectBigTab(new URLFetchable('http://www.biodalliance.org/datasets/ensg-to-desc.bt'), function(bt) {
geneDescriptions = bt;
});
b.addFeatureInfoPlugin(function(f, info) {
if (f.geneId) {
var desc = makeElement('div', 'Loading...');
info.add('Description', desc);
geneDescriptions.index.lookup(f.geneId, function(res, err) {
if (err) {
console.log(err);
} else {
desc.textContent = res;
}
});
}
});
</script>
</head>
<body>
<a href='http://www.ensembl.org/' id='enslink' target='_newtab'>Link to Ensembl</a>
<div id='svgHolder'>Dalliance genome browser goes here. Unless you have an ancient web browser or something.</div>
</body>
</html>