Vaccine Design Report
{% for key, val in (patient_summary | default(patient_info)).items() %}
{{ key }}: {{ val }}
{% endfor %}

{% if input_coverage %}{% include "templates/input_coverage.txt" %}{% endif %}
{% include "templates/products.txt" %}
{% if ranked_candidates is defined %}{% include "templates/ranking.txt" %}{% endif %}
{% if input_coverage %}{% include "templates/source_outcomes.txt" %}{% endif %}

{% if candidate_details | default(true) and variants %}
=== Candidate window details ===
Candidate context only. Final sequences are listed under Emitted products.
{% for v in variants %}
{{ v.num }}) {{ v.short_description }} ({{ v.variant_data['Gene name'] }})
        {% for key, val in v.variant_data.items() %}
        {{ key }}: {{ val }}
        {% endfor %}

        {% for key, val in v.effect_data.items() %}
        {{ key }}: {{ val }}
        {% endfor %}
        {% if v.admission_note %}{{ v.admission_note }}{% endif %}
        {% for section in v.source_evidence_sections %}
        {{ section.title }}
        {% if section.note %}{{ section.note }}{% endif %}
        {% for label, value in section.rows %}{{ label }}: {{ value }}
        {% endfor %}
        {% endfor %}

        Candidate windows:
        {% for p in v.peptides %}
                {{ p.header_display_data.num }}. {{ p.header_display_data.aa_before_mutation }}_{{ p.header_display_data.aa_mutant }}_{{ p.header_display_data.aa_after_mutation }} (score = {{ v.variant_data["Top score"] }})
                  {% for key, val in p.peptide_data.items() %}
                  - {{ key }}: {{ val }}
                  {% endfor %}

                  Predicted target epitopes:
                  {{ p.ascii_epitopes|indent(18) }}

                  {% if include_wt_epitopes and p.wt_epitopes %}
                  Predicted self epitopes:
                  {{ p.ascii_wt_epitopes|indent(18) }}
                  {% endif %}

        {% endfor %}
{% endfor %}
{% endif %}




=== Methods and provenance ===
Prediction evidence
{% for model in prediction_models %}
{{ model.name }} {{ model.version }}: {{ model.status }}
{% endfor %}
Presentation score: the named predictor's presentation output (NetMHCpan: Score_EL).
Presentation score: higher is stronger; presentation percentile: lower is stronger.
Score: Vaxrank's configured per-allele ranking score, shared across predictor rows.
Integrated processing: the named predictor's antigen-processing model, not Pepsickle.
Processing: Pepsickle cleavage annotation; combined is sqrt(C-term * (1 - max internal)).
WT: recorded comparator, not evidence of an observed patient-normal sequence.


{% if input_coverage %}{% include "templates/input_lineage.txt" %}{% endif %}
{% for key, val in patient_info.items() %}{{ key }}: {{ val }}
{% endfor %}
{% if prediction_configuration %}
=== Effective prediction configuration ===
{% for stage in prediction_configuration %}
{{ stage.stage }}: {{ stage.status }}
{% for detail in stage.details %}  {{ detail }}
{% endfor %}
{% endfor %}
{% endif %}

Run arguments
{% for key, val in args %}
  {{ key }}: {{ val }}
{% endfor %}

Package versions
{% for key, val in package_versions.items() %}
  {{ key }}: {{ val }}
{% endfor %}
