{% extends "report_base.html" %}

{% block body %}
<br>
<div class="container">
  <h4>Scout - Institute {{institute.display_name}} - case {{case.display_name}} - {{panel.name_and_version}}: panel extent report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong><br><br>
  {{ hits_panel() }}
  <br>[END OF REPORT]<br><br>
  <a style="text-decoration:none;" href="https://clinical-genomics.github.io/scout" target="_blank" rel="noopener">clinical-genomics.github.io/scout</a>
</div>
{% endblock %}

{% macro hits_panel() %}
<table class="table table-sm">
  <tr>
    <th>Panel details</th>
    <th>Case details</th>
  </tr>
  <tr>
    <td>
      Gene panel: <strong>{{panel.name_and_version}}</strong><br>
      Last updated: <strong>{{ panel.date.strftime('%Y-%m-%d') }}</strong>
      {% if case.outdated_panels and panel.panel_name in case.outdated_panels %}
              <a><span class="badge rounded-pill py-1 bg-warning" data-bs-toggle="popover" data-bs-placement="left" data-bs-html="true" data-bs-content="Panel version used in the analysis ({{panel.version}}) is outdated. Latest panel version is used in variants filtering.<br /><strong>Genes present in case panel and not in latest version</strong>: {{case.outdated_panels[panel.panel_name]['extra_genes']|join(', ') or '-'}}.<br /><strong>Genes present only in latest version</strong>: {{case.outdated_panels[panel.panel_name]['missing_genes']|join(', ') or '-'}}.">!</span></a>
      {% endif %}<br>
      Panel ID: {{ panel.panel_name }}<br>
      Description: {{ panel.description }}<br>
      Number of genes: <strong>{{ panel.genes|length }}</strong><br>
      Institute: {{ panel.institute }} <br>
      Archived: {% if panel.is_archived %}<span class="badge bg-danger rounded-pill">True</span>{% else %}<span class="badge bg-secondary rounded-pill text-white">False</span>{% endif %}<br>
    </td>
    <td>
      Case: <strong>{{case.display_name}}</strong><br>
      Institute: <strong>{{institute.display_name}} - {{institute._id}}</strong><br>
      Status: <strong>{{case.status}}</strong><br>
      Analysis date: {{case.analysis_date}}<br>
      Genome build: {{case.genome_build}}
    </td>
  </tr>
</table>
<br>
<table>
  <tr><th scope="col">Panel genes</th></tr>
  <tr>
    <td>
      <em>{{ panel_genes|sort|join(", ") }}</em>
    </td>
  </tr>
</table>
<br>
{% if case.outdated_panels and panel.panel_name in case.outdated_panels %}
<table>
  <tr><th scope="col">
      <span class="badge rounded-pill badge-sm bg-warning">!</span>Outdated panel</th>
  </tr>
  <tr>
    <td>
      Panel version used in the analysis ({{panel.version}}) is outdated.<br>
      <strong>Genes present in case panel and not in latest version</strong><br>
      {{case.outdated_panels[panel.panel_name]['extra_genes']|join(', ') or '-'}}<br>
      <strong>Genes present only in latest version</strong>
      <br>{{case.outdated_panels[panel.panel_name]['missing_genes']|join(', ') or '-'}}.
    </td>
  </tr>
</table><br>
{% endif %}
{% if variant_hits.str %}
<table>
  <tr><th scope="col">Panel genes investigated for STRs</th></tr>
  <tr>
    <td>
      <em>{{ variant_hits.str|sort|join(", ") }}</em>
    </td>
  </tr>
</table>
<br>
{% endif %}
{% if variant_hits.smn and case.smn_tsv %}
<table>
  <tr><th scope="col">SMN Copy Number</th></tr>
  <tr>
    <td>
      <em>{{ variant_hits.smn|sort|join(", ") }}</em>
    </td>
  </tr>
</table>
{% endif %}
{% endmacro %}