{% extends "template.html" %}


{% block table_of_contents %}
<li><a href="#readqc">Read QA/QC</a></li>
<li><a href="#readmapping">Read Mapping</a></li>
<li><a href="#typing">Haplotype Calling</a></li>
<li><a href="#filters">Genotype Calling</a></li>
{% endblock %}


{% block read_len_fig %}
<img class="center" src="img/read-lengths.png" />
<p class="caption"><strong>Figure 1.1</strong>: Ridge plot showing the length distribution of input reads.</p>
{% endblock %}


{% block read_len_table %}
<p class="title"><strong>Table 1.1</strong>: Uniform read length for each sample.</p>
<table class="half">
    <tr>
        <th>Sample</th>
        <th class="alnrt">Length</th>
    </tr>
    {% for i, row in read_length_table.iterrows() %}
    <tr>
        <td>{{ row.Sample }}</td>
        <td class="alnrt">{{ row.Length }}</td>
    </tr>
    {% endfor %}
</table>
{% endblock %}


{% block read_filter_stats %}
<p>
    Prior to subsequent analysis, reads are filtered for length and ambiguous sequence content.
    Any read comprised of more than {{"{:.0f}".format(ambiguous_read_threshold * 100)}}% ambiguous bases (<code>N</code>) is discarded.
    Reads less than {{"{:,}".format(read_length_threshold)}} bp in length are also excluded from all subsequent analysis.
    (These thresholds can be configured with the <code>--ambiguous-thresh</code> and <code>--length-thresh</code> arguments.)
</p>
<p class="title"><strong>Table 1.2</strong>: Read filtering metrics.</p>
<table>
    <tr>
        <th>Sample</th>
        <th class="alnrt">Total Reads</th>
        <th class="alnrt">Filtered (Ambiguous)</th>
        <th class="alnrt">Filtered (Length)</th>
        <th class="alnrt">Reads Kept</th>
    </tr>
    {% for sample, stats in qc.items() %}
    <tr>
        <td>{{sample}}</td>
        <td class="alnrt">{{stats.total_reads}}</td>
        <td class="alnrt">{{stats.filtered_ambig}}</td>
        <td class="alnrt">{{stats.filtered_length}}</td>
        <td class="alnrt">{{stats.retention}}</td>
    </tr>
    {% endfor%}
</table>
{% endblock %}


{% block read_map_header %}
<p>Filtered reads are aligned to marker reference sequences using <a href="http://bio-bwa.sourceforge.net/bwa.shtml"
        target="_blank">BWA MEM</a> and formatted, sorted, and indexed using <a href="http://www.htslib.org/"
        target="_blank">SAMtools</a>.</p>
{% endblock %}