{% macro gtcall_panel(variant, case) %}
  {% set case_has_capture = ("panel" in case.analysis_types or "wes" in case.analysis_types) %}
  <div class="card panel-default">
    <div class="panel-heading">
      GT call
      {% if variant.is_par %}
        <span class="badge bg-info">PAR</span>
      {% endif %}
    </div>
    <div class="card-body">
    <div class="table-responsive">
      <table class="table table-bordered">
        <thead class="thead table-light">
          <tr>
            <th rowspan="2">Sample</th>
            <th rowspan="2">Genotype (GT)</th>
            <th colspan="2"><div data-bs-toggle="tooltip" title="Unfiltered count of reads that support a given allele.">Allele depth (AD)</div></th>
            {% if variant.category == "cancer" %}
              <th rowspan="2" colspan="1" title="Variant Allele Frequency.">Variant Allele Frequency (VAF)</th>
            {% elif variant.category == "sv" %}
              <th rowspan="2" colspan="1" title="Copy number" scope="copy_number">Copy number</th>
              <th rowspan="2" colspan="1" ><div data-bs-toggle="tooltip" title="SV caller specific quality score. Note different scales for different callers.">SV quality</div></th>
            {% elif variant.category == "str" %}
              <th rowspan="2" colspan="1"><div data-bs-toggle="tooltip"  title="Call support status from Expansion hunter, or STRdrop ratio and probability in parenthesis if available.">Expansion support</div></th>
            {% else %}
	      {% if variant.category == "snv" and (variant.is_mitochondrial or case_has_capture) %}
                <th rowspan="2" colspan="1" title="Variant Allele Frequency.">Variant Allele Frequency (VAF)</th>
	      {% endif %}
              <th rowspan="2" colspan="1"><div data-bs-toggle="tooltip" title="Phred-scaled confidence that the true genotype is the one provided in GT (max=99).">Genotype quality (GQ)</div></th>
            {% endif %}
            <tr>
              <th>Reference</th>
              <th>Alternative</th>
            </tr>
          </tr>
        </thead>
        <tbody>
          {% for sample in variant.samples %}
           <tr{% if sample.is_affected %} class="table-danger"{% endif %}>
              <td>{{ sample.display_name }}</td>
              <td>{{ sample.genotype_call }}</td>
              {% if sample.allele_depths %}
                  {% for number in sample.allele_depths %}
                    <td>
                      {% if number == -1 %}
                        <small>N/A</small>
                      {% else %}
                        {{ number }}
                      {% endif %}
                    </td>
                  {% endfor %}
              {% else %}
                  <td><small>N/A</small></td>
                  <td><small>N/A</small></td>
              {% endif %}

              {% if variant.category == "snv" and (variant.is_mitochondrial or case_has_capture) %}
                <td>
                  {# Using number == number as a test for NaN value numbers here. Given that they exist, NaN values are the only time a number is not considered equal to itself. #}
                  {% if sample.alt_frequency and sample.alt_frequency != -1 and sample.alt_frequency == sample.alt_frequency %}
                    {{ (100*sample.alt_frequency)|round(2) }}%
                  {% else %}
                    N/A
                  {% endif %}
                </td>
              {% endif %}
              {% if variant.category == "cancer" %}
                {% set cancer_var = namespace() %}
                {% if variant.tumor and sample.sample_id == variant.tumor.ind_id %}
                  {% set cancer_var.vaf = variant.tumor.alt_freq|round(4) %}
                {% elif variant.normal and sample.sample_id == variant.normal.ind_id %} <!--normal-->
                  {% set cancer_var.vaf = variant.normal.alt_freq|round(4) %}
                {% else %}
                  {% set cancer_var.vaf = "N/A" %}
                {% endif %}
                <td>{{ cancer_var.vaf }}</td>
              {% else %}
                {% if variant.category == "sv" %}
                  <td>{{ sample.copy_number or "N/A" }}</td>
                  <td>
                  {% if sample.genotype_quality not in ["None", None, "-1", -1] %}
                    {{ sample.genotype_quality }}
                  {% else %}
                    <small>N/A</small>
                  {% endif %} (<small>VQ</small>
                  {% if variant.quality and variant.quality not in ["None", None, "-1", -1] %}
                    {{variant.quality|round(1)}}
                  {% else %}
                    <small>N/A</small>
                  {% endif%})
                  </td>
                {% elif variant.category == "str" %}
                  <td><small>{% if sample.so %}{{ sample.so }}{% elif sample.sdr and sample.sdp %}{{ sample.sdr|round(4) }} ({{ sample.sdp|round(4)}}){% endif %}</small></td>
                {% else %}
                  <td>{{ sample.genotype_quality }}</td>
                {% endif %}
              {% endif %}
            </tr>
          {% endfor %}
        </tbody>
      </table>
    </div>
    <div class="panel-footer">
       {% for filter in variant.filters %} <!-- collect info from variant's filters (PASS) -->
        <span class="badge bg-{{ filter.label_class }}" data-bs-toggle="tooltip" data-bs-placement="top" title="{{ filter.description }}">
          {{ filter.label }}
        </span>
      {% endfor %}
      {% for name, caller in variant.callers %}
        <span class="badge {% if caller == 'Pass' %}bg-success{% elif 'Filtered' in caller %}bg-secondary{% else %}bg-black{% endif %}">
        {{ name }}: {{ caller }}
        </span>
      {% endfor %}
    </div>
    </div>
  </div>
{% endmacro %}

{% macro str_db_card(variant) %}
  <div class="card panel-default">
    <div class="panel-heading">STR locus details</div>
    <div class="card-body">
      <table class="table" aria-label="STR locus details">
        <thead class="thead table-light">
            <tr>
              <th scope="col">Source</th>
              <th scope="col">Value</th>
            </tr>
          </thead>
          <tbody>
            <tr><td>Normal max</td><td>{{ variant.str_normal_max }}</td></tr>
            <tr><td>Pathologic min</td><td>{{ variant.str_pathologic_min }}</td><tr>
            {% if variant.str_status == 'full_mutation' %}
              <tr class="bg-danger">
            {% elif variant.str_status == 'pre_mutation' %}
              <tr class="bg-warning">
            {% else %}
              <tr>
	          {% endif %}
              <td>Motif copies</td><td>{{ variant.str_mc or "." }} <span class="badge bg-secondary text-white">{{ variant.str_status }}</span></td>
            </tr>
            <tr><td colspan=2>&nbsp;</td></tr>
            {% if variant.str_swegen_mean %}
              <tr><td>SweGen Z-score</td><td>
                {% if variant.str_mc %}
                  {{ ((variant.str_mc - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
                {% endif %}
              </td></tr>
              <tr><td>SweGen mean</td><td>{{variant.str_swegen_mean|round(2)}}</td></tr>
              <tr><td>SweGen std</td><td>{{variant.str_swegen_std|round(2)}}</td></tr>
              <tr><td colspan=2>&nbsp;</td></tr>
            {% endif %}
            {% for gene in variant.genes %}
              {% if gene.stripy_link %}
                <tr><td>
                  <a href="{{ gene.gnomad_str_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">gnomAD</a>
                </td><td>{{ gene.hgnc_symbol }}</td></tr>
              {% endif %}
              {% if gene.stripy_link %}
                <tr><td>
                  <a href="{{ gene.stripy_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">STRipy</a>
                </td><td>{{ gene.hgnc_symbol }}</td></tr>
              {% endif %}
            {% endfor %}
          </tbody>
        </table>
    </div>
  </div>
{% endmacro %}

{% macro frequencies_table(variant) %}
<table class="table table-sm align-middle mb-1" style="font-size: 0.875rem;">
  <thead class="table-light">
    <tr>
      <th scope="col" class="py-1 px-2">Source</th>
      <th scope="col" class="py-1 px-2">Frequency</th>
    </tr>
  </thead>
  <tbody>
    {% for freq_name, value, link in variant.frequencies %}
      <tr>
        <td class="py-1 px-2">
          {% if link %}
            <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
          {% else %}
            {{ freq_name }}
          {% endif %}
        </td>
        <td class="py-1 px-2">
          {% if value %}
            <span class="badge bg-secondary" style="font-size: 0.75rem;">{{ value|human_decimal }}</span>
          {% else %}
            -
          {% endif %}
        </td>
      </tr>
    {% endfor %}
  </tbody>
</table>
{% endmacro %}

{% macro frequencies(variant) %}
  <div class="card panel-default">
    <div class="panel-heading">Frequencies</div>
    <div class="card-body">
      {{ frequencies_table(variant) }}
    </div>
  </div>
{% endmacro %}

{% macro observation_badge(observed_case) %}

  {% if observed_case.variant and observed_case.variant.category == "snv"%}
  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
  {% elif observed_case.variant and observed_case.variant.category == "sv"%}
  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
  {% else %}
  <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
    <span class="ml-3 badge rounded-pill bg-light text-dark">{{ observed_case.case.display_name }}</span>
  </span>
  {% endif %}

{% endmacro %}

{% macro observations_panel(variant, observations, case) %}
  <div class="card panel-default">
    <div class="panel-heading d-flex justify-content-between">
      <a href="https://github.com/moonso/loqusdb" target="_blank">Local observations</a>
      <span data-bs-toggle="tooltip" title="Nr of observations is the total number of cases where the variant occurs in the loqusdb instance. Names of collaborator cases are shown.">?</span>
    </div>
    <div class="card-body">
      <table class="table">
        <thead class="thead table-light">
          <tr>
            <th scope="col">ID</th>
            <th scope="col">Nr obs.</th>
            <th scope="col">Nr homo.</th>
            <th scope="col">Total nr.</th>
          </tr>
        </thead>
        <tbody>
          {% for loqusid, obs in observations.items() %}
              {% set obs_count = obs.observations %}
              <tr>
                <td>{{ loqusid }}</td>
               <td>{{ render_obs(obs_count) }}</td>
               <td>{{ render_obs(0 if obs_count == 0 else obs.homozygote) }}</td>
               <td>{{ render_obs(obs.total) }}</td>
             </tr>
            {% if obs.cases or obs.observations == 1 %}
              <tr>
                <td colspan="4">
                  {% if obs.observations == 1 %}
                  {% if obs.case_match == True %}
                     Observed only in this case
                     <span id="case_match_tooltip"  data-bs-toggle='tooltip' title="Subsequent analysis of the same individual or multiple occurrences within the same family will usually not result in an increased observation count, even if performed by different institutes.">
                       <i class="mx-1 fas fa-info-circle"></i>
                     </span>
                  {% elif obs.case_match == False %}
                     Observed in one other case
                     <span id="case_mismatch_tooltip"  data-bs-toggle='tooltip' title="Low sequencing quality for the variant or previous loqusdb upload of data from the same individuals may prevent the current case from occurring in loqusdb">
                       <i class="mx-1 fas fa-info-circle"></i>
                     </span>
                  {% endif %}
                  {% endif %}
                  {% for observed_case in obs.cases %}
                    {% if loop.index <= 10 %}
                      {{ observation_badge(observed_case) }}
                    {% endif %}
                  {% endfor %}

                  {% if obs.cases|length > 10 %}
                    <span class="collapse" id="additionalCases_{{ loqusid }}">
                      {% for observed_case in obs.cases %}
                        {% if loop.index > 10 %}
                          {{ observation_badge(observed_case) }}
                        {% endif %}
                      {% endfor %}
                    </span>
                    <button class="btn btn-link p-0 toggle-button" type="button" data-bs-toggle="collapse" href="#additionalCases_{{ loqusid }}">
                      <span class="toggle-text">Show more/less</span>
                    </button>
                  {% endif %}
                </td>
              </tr>
            {% endif %}
          {% endfor %}
        </tbody>
      </table>
    </div>
  </div>
{% endmacro %}

{% macro render_obs(value) %}
  {% if value is not defined or value is none or value == -1 %}
    N/A
  {% else %}
    {{ value }}
  {% endif %}
{% endmacro %}

{% macro old_observations_table(variant) %}
  {% macro render_freq(freq, obs, nr_cases) -%}
    {% if freq is defined and freq is not none %}
      {{ freq|round(6) }}
    {% elif nr_cases and obs is defined and obs is not none and obs != -1 %}
      {{ (obs / nr_cases)|round(5) }}
    {% elif nr_cases %}
      0 / {{ nr_cases }}
    {% else %}
      N/A
    {% endif %}
  {%- endmacro %}

  <table class="table">
    <thead class="thead table-light">
      <tr>
        <th scope="col">Local archive</th>
        <th scope="col">Nr obs.</th>
        <th scope="col">Nr homo.</th>
        <th scope="col">Frequency</th>
      </tr>
    </thead>
    <tbody>
      {% set obs_count = variant.local_obs_old %}
      <tr>
        <td>RD</td>
        <td>{{ render_obs(obs_count) }}</td>
        <td>{{ render_obs(0 if obs_count == 0 else variant.local_obs_hom_old) }}</td>
        <td>{{ render_freq(variant.local_obs_old_freq, variant.local_obs_old, variant.local_obs_old_nr_cases) }}</td>
      </tr>
      {% if variant.category in ['cancer', 'cancer_sv'] %}
        {% set obs_count = variant.local_obs_cancer_germline_old %}
        <tr>
          <td>Cancer Germline</td>
          <td>{{ render_obs(obs_count) }}</td>
          <td>{{ render_obs(0 if obs_count == 0 else variant.local_obs_cancer_germline_hom_old) }}</td>
          <td>{{ render_freq(variant.local_obs_cancer_germline_old_freq, variant.local_obs_cancer_germline_old, variant.local_obs_cancer_germline_old_nr_cases) }}</td>
        </tr>
        {% set obs_count = variant.local_obs_cancer_somatic_old %}
        <tr>
          <td>Cancer Somatic</td>
          <td>{{ render_obs(obs_count) }}</td>
          <td>{{ render_obs(0 if obs_count == 0 else variant.local_obs_cancer_somatic_hom_old) }}</td>
          <td>{{ render_freq(variant.local_obs_cancer_somatic_old_freq, variant.local_obs_cancer_somatic_old, variant.local_obs_cancer_somatic_old_nr_cases) }}</td>
        </tr>
        {% set obs_count = variant.local_obs_cancer_somatic_panel_old %}
        <tr>
          <td>Cancer Somatic panel</td>
          <td>{{ render_obs(obs_count) }}</td>
          <td>N/A</td>
          <td>{{ render_freq(variant.local_obs_cancer_somatic_panel_old_freq, variant.local_obs_cancer_somatic_panel_old, None) }}</td>
        </tr>
      {% endif %}
    </tbody>
  </table>
{% endmacro %}

{% macro old_observations(variant, obs_date) %}
{% if "SHOW_OBSERVED_VARIANT_ARCHIVE" in config and config["SHOW_OBSERVED_VARIANT_ARCHIVE"] == true %}
  <div class="card panel-default">
    <div class="panel-heading">
      <a href="https://github.com/moonso/loqusdb" target="_blank" data-bs-toggle="tooltip" title="Local observations annotated from an archive copy of the loqusdb local frequency database. Only variants above a quality threshold are included, and each case is included only once. {% if variant.local_obs_old_desc %} {{variant.local_obs_old_desc}} {% endif %}">Local observations (archive {{ obs_date or variant.local_obs_old_date or "version"}})</a>
    </div>
    <div class="card-body">
      {{ old_observations_table(variant) }}
    </div>
  </div>
{% endif %}
{% endmacro %}

{% macro severity_list(variant) %}
  <div class="card panel-default">
    <div class="panel-heading">Severity</div>
    <div class="card-body">
      <ul class="list-group">
        <li class="list-group-item">
          <a href="https://sift.bii.a-star.edu.sg/www/SIFT_help.html" target="_blank">SIFT</a>
          <span class="float-end">
            {% if variant.sift_predictions  %}
              {{ variant.sift_predictions|join(', ') }}</span>
            {% else %}
               {{ "-" }}
            {% endif %}
          </span>
        </li>
        <li class="list-group-item">
          <a href="https://sites.google.com/site/revelgenomics/about" target="_blank" data-bs-toggle="tooltip"
            title="An ensemble score based on 13 individual scores for predicting the pathogenicity of missense variants. Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect">REVEL score</a>
          {% if variant.revel and variant.revel != "-" %}
            <span class="badge float-end bg-{{variant.revel|get_label_or_color_by_score('revel', 'color')}}" data-bs-toggle="tooltip" title="{{variant.revel|get_label_or_color_by_score('revel', 'label')}}">
              {{ variant.revel }}
            </span>
          {% else %}
            <span class="float-end">
              {{ "-" }}
            </span>
          {% endif %}
        </li>
        <li class="list-group-item">
          <a href="http://database.liulab.science/dbNSFP" target="_blank" data-bs-toggle="tooltip"
             title="REVEL scores were ranked among all REVEL scores in dbNSFP. The REVEL rank score is the ratio of the rank of the score over the total number of REVEL scores in dbNSFP">REVEL rank score</a>
          <span class="float-end">
          {% if variant.revel_score  %}
             {{ variant.revel_score }}
          {% else %}
             {{ "-" }}
          {% endif %}
          </span>
        </li>
        <li class="list-group-item">
          <a href="http://genetics.bwh.harvard.edu/pph2/" target="_blank">Polyphen</a>
          <span class="float-end">
          {% if variant.polyphen_predictions %}
            {{ variant.polyphen_predictions|join(', ') }}
          {% else %}
             {{ "-" }}
          {% endif %}
          </span>
        </li>
        <li class="list-group-item">
          SPIDEX
          <span class="float-end">{{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }}</span>
        </li>
        <li class="list-group-item">
          {% set spliceai_highest = variant.spliceai_scores | spliceai_max %}
          <a href="{{ variant.spliceai_link }}" target="_blank" rel="noopener">SpliceAI</a> <a href="https://github.com/Illumina/SpliceAI" target="_blank" rel="noopener">DS max</a>
          {% if spliceai_highest is not none %}
            <span class="badge bg-{{ spliceai_highest | get_label_or_color_by_score('spliceai', 'color') }} float-end" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="bottom"
                title="<strong>
                  {% for entry in variant.spliceai_scores %}
                    {% if entry is not none %}
                      SpliceAI highest delta score {{ entry }} </strong> at position {{ variant.spliceai_positions[loop.index0]}} relative to this variant. {{ spliceai_highest | get_label_or_color_by_score('spliceai', 'label')}} according to Walker et al 2023.
                      {% if variant.spliceai_predictions[loop.index0] %}
                        <br>All scores and positions(relative to variant):<br>
                        {{ variant.spliceai_predictions[loop.index0] }} <br>
                      {%  endif %}
                      <br>
                    {% else %}
                      No SpliceAI positions annotated for this variant.
                    {% endif %}
                  {% endfor %}
                ">
                {{ variant.spliceai_scores|join(', ') }}
            {% else %}
              <span class="float-end">{{ "-" }}
            {% endif %}
          </span>
        </li>
      </ul>
    </div>
  </div>
{% endmacro %}

{% macro conservations(variant) %}
  <div class="card panel-default">
    <div class="panel-heading">Conservation</div>
    <div class="card-body">
      <ul class="list-group">
        <li class="list-group-item">
          PHAST
          <span class="float-end">{{ variant.phast_conservation|join(', ') or '-' }}</span>
        </li>
        <li class="list-group-item">
          GERP
          <span class="float-end">{{ variant.gerp_conservation|join(', ') or '-' }}</span>
        </li>
        <li class="list-group-item">
          phyloP
          <span class="float-end">{{ variant.phylop_conservation|join(', ') or '-' }}</span>
        </li>
      </ul>
    </div>
  </div>
{% endmacro %}


{% macro mappability_list(variant) %}
  {% set superdups_fracmatches = [] %}
  {% for gene in variant.genes %}
    {% for transcript in gene.transcripts %}
      {% if transcript.superdups_fracmatch %}
        {% for superdup in transcript.superdups_fracmatch %}
          {% do superdups_fracmatches.append(superdup) %}
        {% endfor %}
      {% endif %}
    {% endfor %}
  {% endfor %}
  {% set superdups_fracmatches = superdups_fracmatches|sort %}
  {% if superdups_fracmatches %}
    <li class="list-group-item">
      <span>mapping to {{superdups_fracmatches|length}} segm. dups. (min matching:{{ superdups_fracmatches|first|float|round(3) }}, max matching:{{ superdups_fracmatches|last|float|round(3) }})</span>
    </li>
  {% else %}
    <li class="list-group-item">
      <p class="card-text">-</p>
    </li>
  {% endif %}
{% endmacro %}

{% macro mappability(variant) %}
  <div class="card panel-default">
    <div class="panel-heading">Mappability (<a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=genomicSuperDups" target="_blank">fracMatch</a>)</div>
    <div class="panel-body">
      <ul class="list-group">
        {{ mappability_list(variant) }}
      </ul>
    </div>
  </div>
{% endmacro %}