{% import "bootstrap/wtf.html" as wtf %} {% from "utils.html" import comments_table %} {% macro compounds_table(institute, case, compounds) %} {% for compound in compounds %} {% endfor %}
Variant Combined score Rank score Gene annotation Func. annotation
{% if compound.not_loaded %} {{ compound.display_name }} (not loaded) {% else %} {{ compound.display_name|truncate(20, True) }} {% endif %} {{ compound.combined_score }} {{ compound.rank_score }} {% for annotation in compound.region_annotations %} {{ annotation }}
{% endfor %}
{% for annotation in compound.functional_annotations %} {{ annotation }}
{% endfor %}
{% endmacro %} {% macro svs_table(institute, case, overlapping) %} {% for sv in overlapping %} {% endfor %}
Region Type Length Rank score
{{ sv.chromosome }}{{ sv.cytoband_start }} {{ sv.sub_category }} {{ sv.length if sv.length < 100000000000 else "-" }} {{ sv.rank_score }}
{% endmacro %} {% macro modal_causative(case, institute, variant) %} {% endmacro %} {% macro snv_filters(form, institute, case)%}
{{ form.gene_panels.label}} {{ form.gene_panels(class="selectpicker") }}
{{ form.symbol_file.label(class="control-label", data_toggle="tooltip", data_placement="left", title="Load an HGNC gene symbol list file; a text file with one gene symbol starting each row. Extra columns separated with tab are ignored. Comment rows starting with # are ignored.") }} {{ form.symbol_file(class="form-control-file") }}
{{ form.region_annotations.label(class="control-label") }} {{ form.region_annotations(class="selectpicker") }}
{{ form.functional_annotations.label(class="control-label") }} {{ form.functional_annotations(class="selectpicker") }}
{{ form.genetic_models.label(class="control-label") }} {{ form.genetic_models(class="selectpicker") }}
{{ form.hgnc_symbols.label(class="control-label") }} {{ form.hgnc_symbols(class="form-control") }}
{{ form.cadd_score.label(class="control-label") }} {{ form.cadd_score(class="form-control") }}
{{ form.cadd_inclusive.label(class="control-label", data_toggle="tooltip", data_placement="top", title="Include empty CADD") }}
{{ form.cadd_inclusive() }}
{{ form.spidex_human.label(class="control-label") }} {{ form.spidex_human(class="selectpicker") }}
{{ form.clinsig.label(class="control-label") }} {{ form.clinsig(class="selectpicker") }}
{{ form.clinsig_confident_always_returned.label(class="control-label", data_toggle="tooltip", data_placement="top", title="Always show selected CLINSIG entries with trusted revision status levels.") }}
{{ form.clinsig_confident_always_returned() }}
{{ form.gnomad_frequency.label(class="control-label") }} {{ form.gnomad_frequency(class="form-control") }}
{{ form.local_obs.label(class="control-label") }} {{ form.local_obs(class="form-control") }}
{{ wtf.form_field(form.chrom) }}
{{ wtf.form_field(form.start) }}
{{ wtf.form_field(form.end) }}
{{ form.filter_variants(class="btn btn-primary form-control") }}
{{ form.clinical_filter(class="btn btn-outline-secondary form-control") }}
{{ form.export(class="btn btn-warning form-control") }}
{{ stash_filter_buttons(form, institute, case) }}
{% endmacro %} {% macro sv_filters(form, institute, case) %}
{{ form.gene_panels.label(class="control-label") }} {{ form.gene_panels(class="selectpicker") }}
{{ form.svtype.label(class="control-label") }} {{ form.svtype(class="form-control selectpicker") }}
{{ form.region_annotations.label(class="control-label") }} {{ form.region_annotations(class="selectpicker") }}
{{ form.functional_annotations.label(class="control-label") }} {{ form.functional_annotations(class="selectpicker") }}
{{ form.genetic_models.label(class="control-label") }} {{ form.genetic_models(class="selectpicker") }}
{{ form.hgnc_symbols.label(class="control-label") }} {{ form.hgnc_symbols(class="form-control") }}
{{ form.size.label(class="control-label") }} {{ form.size(class="form-control", type="number") }}
{{ form.size_shorter.label(class="control-label") }}
{{ form.size_shorter() }}
{{ form.decipher.label(class="control-label") }}
{{ form.decipher() }}
{{ form.clinsig.label(class="control-label") }} {{ form.clinsig(class="selectpicker") }}
{{ form.gnomad_frequency.label(class="control-label") }} {{ form.gnomad_frequency(class="form-control") }}
{{ form.clingen_ngi.label(class="control-label") }} {{ form.clingen_ngi(class="form-control") }}
{{ form.swegen.label(class="control-label") }} {{ form.swegen(class="form-control") }}
{{ form.chrom.label(class="control-label") }} {{ form.chrom(class="form-control") }}
{{ wtf.form_field(form.start) }}
{{ wtf.form_field(form.end) }}
{{ form.filter_variants(class="btn btn-primary form-control") }}
{{ form.clinical_filter(class="btn btn-outline-secondary form-control ") }}
{{ form.export(class="btn btn-warning form-control") }}
{{ stash_filter_buttons(form, institute, case) }}
{% endmacro %} {% macro cancer_filters(form, institute, case) %} {{ form.csrf_token }} {{ form.variant_type() }}
{{ form.gene_panels.label(class="control-label") }} {{ form.gene_panels(class="selectpicker") }}
{{ form.region_annotations.label(class="control-label") }} {{ form.region_annotations(class="selectpicker") }}
{{ form.functional_annotations.label(class="control-label") }} {{ form.functional_annotations(class="selectpicker") }}
{{ form.genetic_models.label(class="control-label") }} {{ form.genetic_models(class="selectpicker") }}
{{ form.clinsig.label(class="control-label") }} {{ form.clinsig(class="selectpicker") }}
{{ form.mvl_tag.label(class="control-label") }}
{{ form.mvl_tag() }}
{{ form.hgnc_symbols.label(class="control-label") }} {{ form.hgnc_symbols(class="form-control") }}
{{ form.cadd_score.label(class="control-label") }} {{ form.cadd_score(class="form-control") }}
{{ form.cadd_inclusive.label(class="control-label", data_toggle="tooltip", data_placement="top", title="Include empty CADD") }}
{{ form.cadd_inclusive() }}
{{ form.gnomad_frequency.label(class="control-label") }} {{ form.gnomad_frequency(class="form-control") }}
{{ form.depth.label(class="control-label") }} {{ form.depth(class="form-control") }}
{{ form.alt_count.label(class="control-label") }} {{ form.alt_count(class="form-control") }}
{{ form.control_frequency.label(class="control-label") }} {{ form.control_frequency(class="form-control") }}

{{ stash_filter_buttons(form, institute, case) }}
{% endmacro %} {% macro modal_prompt_filter_name(form) %} {% endmacro %} {% macro stash_filter_buttons(form, institute, case) %}
{{ modal_prompt_filter_name(form) }}
{{ form.filters(class="form-control") }}
{{ form.load_filter(class="btn btn-secondary", disabled=form.filters.choices|length==0) }} {{ form.delete_filter(class="btn btn-secondary bg-danger", data_toggle="tooltip", data_placement="top", title="Delete selected filter for this institute.", disabled=form.filters.choices|length==0) }}
{% endmacro %} {% macro tier_cell(variant, manual_rank_options, cancer_tier_options) %} {% if variant.cancer_tier %} {% if variant.cancer_tier == '1A' %} {% set label_class = 'danger' %} {% elif variant.cancer_tier == '1B' %} {% set label_class = 'danger' %} {% elif variant.cancer_tier == '2A' %} {% set label_class = 'warning' %} {% elif variant.cancer_tier == '2B' %} {% set label_class = 'warning' %} {% elif variant.cancer_tier == '3' %} {% set label_class = 'primary' %} {% elif variant.cancer_tier == '4' %} {% set label_class = 'default' %} {% endif %} {{ cancer_tier_options[variant.cancer_tier].label }} {% endif %} {% if variant.manual_rank %} {% if variant.manual_rank == 1 %} {% set label_class = 'default' %} {% elif variant.manual_rank == 2 %} {% set label_class = 'info' %} {% elif variant.manual_rank == 3 %} {% set label_class = 'primary' %} {% elif variant.manual_rank == 4 %} {% set label_class = 'warning' %} {% elif variant.manual_rank == 5 %} {% set label_class = 'danger' %} {% endif %} {{ manual_rank_options[variant.manual_rank].label }} {% endif %} {% endmacro %} {% macro cell_rank(variant, institute, case, form, manual_rank_options) %} {% if variant.category in ("sv", "cancer_sv") %} {% else %} {% endif %} {{ variant.variant_rank }}  {% set comment_count = variant.comments.count() %} {% if variant.acmg_classification %} {{ variant.acmg_classification.short }} {% endif %} {% if variant.manual_rank %} {{ manual_rank_options[variant.manual_rank].label }} {% endif %} {% if variant.evaluations %} {% for evaluation in (variant.evaluations or []) %} {{ evaluation.classification.short }} {% endfor %} {% endif %} {% if form.variant_type.data == 'research' %} {% if variant.clinical_assessments %} {% for assessment in variant.clinical_assessments %} {{ assessment.label }} {% endfor %} {% endif %} {% endif %} {% if comment_count > 0 %} {% set comments_content = comments_table(institute, case, variant.comments, variant._id) %} {{ comment_count }} {% if 'GLOBAL' in comments_content %} {% endif %} {% endif %} {% if variant._id in case.suspects %} {% endif %} {% endmacro %}