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bam_matcher_html_template
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bam_matcher_html_template
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<!DOCTYPE html>
<html>
<head>
<style>
body {background-color:white;
font-size:12px;
}
h1 {color:blue;
font-size:20px;
}
p {color:black;
font-size:16px}
table {font-size:12px}
th {text-align:left}
#b {text-align:center;
border-width:1px;
border-style:solid;
border-color:black;
}
#c {text-align:center;
color:blue}
#d {text-align:center}
</style>
</head>
<body>
<h1>Compare BAM files using common SNPs</h1>
<h2>Input files and parameters</h2>
<table>
<tr><th>BAM1:</th><td>${BAM1}   </td><td>(${bam1_cached})</td></tr>
<tr><th>BAM2:</th><td>${BAM2}   </td><td>(${bam2_cached})</td></tr>
<tr><th>Minimum depth:   </th><td>${DP_THRESH}</td></tr>
<tr><th>Caller</th><td>${caller}</td></tr>
<tr><th>Variants compared</th><td>${variants}</td></tr>
</table>
<hr width="50%" align="left">
<h2>Results</h2>
<table>
<tr><th width="250px">Total number of positions compared:    </th><td>${total}</td></tr>
<tr><th>Percentage of common genotypes:</th><td>${frac_common}</td></tr>
</table>
</br>
<hr width="50%" align="left">
<table>
<tr><th width="250px">Positions with same genotype:</th><td>${ct_common}</td></tr>
<tr><th> Break-down:</th></tr>
<tr><th> Homozygous sites</th><td>${comm_hom_ct}</td></tr>
<tr><th> Heterozygous sites</th><td>${comm_het_ct}</td></tr>
</table>
</br>
<hr width="50%" align="left">
<table>
<tr><th width="250px">Positions with different genotype:</th><td>${ct_diff}</td></tr>
<tr><th> Break-down:</th></tr>
</table>
<table id="b">
<tr><td colspan="2" rowspan="2" bgcolor="grey"></td>
<th id="c" colspan="3" style="height:30px" bgcolor="lightgrey">BAM 1</th>
</tr>
<tr><th style="height:30px; width:60px" id="d">het</th>
<th style="width:60px" id="d">hom</th>
<th style="width:60px" id="d">subset</th>
</tr>
<tr><th id="c" rowspan="3" bgcolor="lightgrey">BAM 2</th>
<th style="height:30px" id="d">het</th>
<td id="d">${diff_het_ct}</td>
<td id="d">${diff_hom_het_ct}</td>
<td id="d">${diff_1sub2_ct}</td>
</tr>
<tr><th style="height:30px" id="d">hom</th>
<td id="d">${diff_het_hom_ct}</td>
<td id="d">${diff_hom_ct}</td>
<td id="d">-</td>
</tr>
<tr><th style="height:30px" id="d">subset</th>
<td id="d">${diff_2sub1_ct}</td>
<td id="d">-</td>
<td id="d">-</td>
</tr>
</table>
<hr width="50%" align="left">
<h2>Conclusion</h2>
<p>${judgement}
</body>
</html>