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<html>
<head>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="http://code.jquery.com/jquery-1.10.2.min.js"></script>
<script src="VQI_GenomeBrowser.js"></script>
<script src="FileSaver.min.js"></script>
<script src="jquery.qtip.min.js"></script>
<link href="jquery.qtip.min.css" rel="stylesheet" type="text/css" />
<!-- Latest compiled and minified CSS -->
<!-- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"> -->
<link rel="stylesheet" href="bootstrap.min.css">
<link rel="stylesheet" href="menu.css">
<!-- Latest compiled and minified JavaScript -->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
</head>
<body>
<div id="test">
</div>
<div id="test2">
</div>
<footer>
<script type="text/javascript">
var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php');
//insert path to file and indexfile
/*obj.addTrack([], "fasta", "fasta",
{ file : "/Users/corywang/Downloads/hg19.fa.txt",
indexFile : "/Users/corywang/Downloads/hg19.fa.fai.txt"});
obj.addTrack([], "cpg", "cpg",
{fileHandle : "upload1437097194,upload1437098473,upload1437098556"});
obj.addTrack([], "HG19", "bed", {fileHandle : "upload1436481988"});
obj.addTrack([], "Tile2 Content Snp", "bed",
{ fileHandle : "upload1436411775",
exportable : true});*/
var genomes = {
"HG19":{
/*fasta: {fasta: "../../genome/hg19.fa", index: "../../genome/hg19.fa.fai"},
genes: {file: "../../genome/hg19_genes.txt", table_name:'hg19_gene_annotation'},
cpg: {file: "../../genome/hg19_genes.txt", table_name:'hg19_cpg'},*/
fasta: {fasta: ""},
genes: {file: "hg19_refgene.txt", table_name: "hg19_refgene"},
// cpg: {file: "cpg_site_hg19.txt,shelve_hg19.txt,shoer_hg19.txt", table_name: "cpg_site_hg19,shelve_hg19,shoer_hg19"},
//custom: {file: "", table_name:'upload1436411775'}
}
// "MM9":{
// fasta: {fasta: "/Users/corywang/Downloads/mm9.fa.txt", index: "/Users/corywang/Downloads/mm9.fa.fai.txt"},
// //genes: {file: "../../genome/mm9/mm9_genes.txt", table_name:'mm9_gene_annotation'},
// // gene_annotation: {label: 'mm9', table_name:'mm9_gene_annotation'},
// },
};
obj.loadGenomes(genomes); //loads the genomes based on the datastructure described above
setTimeout(function(){ hs()}, 1000);
function hs (){
obj.setGenome("HG19");
}
// obj.addTrack("HG19_Custom","Custom",[["CHROM", "CHROM_START" ,"CHROM_END" , "GENESYMBOL", "SCORE", "STRAND"],["chr1" , "896004" , "896005" , "." , "0" , "+"]],true);
//obj.setGenome("HG19");
// obj.setGenome("MM9"); //should set hg19 genome in dropdown and display fasta, cpg and genes tracks.
// addTrack(); should add track using the data array supplied.
</script>
</footer>
</body>
</html>
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