{% extends "layout.html" %} {% from "utils.html" import comments_table, pedigree_panel %} {% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general %} {% from "variant/buttons.html" import reviewer_button%} {% from "variants/utils.html" import cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters, filter_script_main %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - STR variants {% endblock %} {% block css %} {{ super() }} {{ external_stylesheets() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block top_nav_right %} {{ super() }} {% endblock %} {% block content_main %}
{{ pagination_hidden_div(page) }}
{{ filter_form_footer(form, result_size, total_variants, more_variants, page, variants|length, institute) }}
{% set ns = namespace(allele0='') %} {% for variant in variants %} {% if variant.chromosome + variant.position|string != ns.allele0 %} {% endif %} {% set ns.allele0 = variant.chromosome + variant.position|string %} {% if variant.dismiss_variant %} {% elif 'causatives' in case and variant._id in case.causatives %} {% elif variant.str_status == 'normal' %} {% elif variant.str_status == 'full_mutation' %} {% elif variant.str_status == 'pre_mutation' %} {% else %} {% endif %} {% else %} {% endfor %}
Index Repeat locus Reference repeat unit Estimated size Reference size Status Genotype Chr. Position
{{ variant.str_display_ru or variant.str_ru }} {{ variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "") }} {{ variant.str_ref }} {{ str_status(variant) }} {% for sample in variant.samples %} {% if sample.genotype_call != "./." %}
{{ sample.display_name }}
{{ sample.genotype_call }}

{% endif %} {% endfor %}
{{ variant.chromosome }} {{ variant.position|human_longint|safe }} {{ reviewer_button(case,variant,case_groups,institute._id) }} {% if case.bam_files %} IGV viewer {% else %} {% endif %}
No matching variants
{{ pagination_footer(more_variants, page) }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %} {% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %} {% endblock %} {% block scripts %} {{ super() }} {{ external_scripts() }} {{ filter_script_main(cytobands) }} {% endblock %} {% macro str_status(variant) %} ", "")|int - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }} SweGen mean{{variant.str_swegen_mean|round(2)}} SweGen std{{variant.str_swegen_std|round(2)}} {% endif %} {% endif %} {% if not variant.str_normal_max %}
Normal range not provided. Consider updating to a new version of Stranger.
{% endif %}" title="">{{ variant.str_status }}
{% endmacro %} {% macro str_locus_info(variant) %} {{ variant.str_repid }} {% for gene in variant.genes %} S G {% endfor %} {% endmacro %}