{#
  Reusable section fragments shared by the single-sample (report.html) and
  longitudinal (timeline.html) reports. Each macro only places already-formatted,
  HTML-safe values from the render context (see allomix.html.context); the number
  formatting comes from the registered Jinja filters/globals (pct, pval, ci,
  count, badge, ...). No analysis happens here.

  A lab can override this file via --template to restructure or reword any
  section while keeping the rest of the built-in report.
#}

{# A small, collapsed "how this works" disclosure. Body supplied by the caller. #}
{% macro help(summary) %}
<details class="help"><summary>{{ summary }}</summary>
<div class="help-body">{{ caller() }}</div>
</details>
{% endmacro %}

{# Single-sourced "how it works" prose. Each is emitted inline in the HTML report
   (next to the section it explains) and collected into the PDF "Methods and
   notes" appendix, so the wording lives in exactly one place. #}
{% macro help_fractions() %}
{% call help("How the donor and host fractions are estimated") %}
<p>The donor fraction is a maximum-likelihood estimate from the alternate and
reference read depths at informative markers (loci where the host and donor
genotypes differ), following Crysup and Woerner (2022). The host (recipient)
fraction is the remainder. The 95% confidence interval reflects sampling at the
sequenced depth.</p>
<p>Limit of blank is the highest donor fraction expected from a true-zero sample
at this sample's depth and marker set; limit of detection is the lowest fraction
reliably distinguished from blank. Both are specific to this sample.</p>
{% endcall %}
{% endmacro %}

{% macro help_host_presence() %}
{% call help("How host-presence detection works") %}
<p>At markers where every donor is homozygous for the same allele and the host
carries the other allele, that donor-absent allele appears only at the
sequencing-error background in a pure-donor sample. A one-sided test (a
likelihood ratio, with a pooled-Poisson cross-check) asks whether the observed
donor-absent reads exceed that background, that is, whether any host signal is
present.</p>
<p>This answers "is the host detectable?" directly, separately from the size of
the donor fraction estimated above, and is most informative near the detection
limit.</p>
{% endcall %}
{% endmacro %}

{% macro help_qc() %}
{% call help("How the quality-control checks work") %}
<p><strong>Goodness-of-fit</strong> compares the observed allele depths to those
predicted by the fitted fraction; a low p-value means the single-fraction model
fits poorly (an unexpected marker, an extra contributor, or a genotyping error).</p>
<p><strong>Contamination</strong> measures third-party DNA at markers where the
host and every donor share the same homozygote: minor-allele reads there cannot
come from either contributor, so their excess over the sequencing-error floor
estimates contamination (for example index hopping or cross-contamination).</p>
<p><strong>Sample-swap</strong> counts those same shared-homozygote sites where
the minor allele is individually significant; many such sites indicate a whole
extra genome (a swap or wrong-patient VCF).</p>
<p><strong>Shared-het balance</strong> checks the admixture allele fraction at
markers heterozygous in the host and every donor, where it should sit near 50%
whatever the mixing fraction. Many sites skewed away from balance point to
contamination, copy-number or allelic imbalance, or a sample mix-up.</p>
<p><strong>Relatedness</strong> is a kinship coefficient between the reference
samples, compared against the declared relationship to catch mislabelled or
unexpectedly related inputs.</p>
<p>The <strong>robust refit</strong> re-fits after dropping markers whose
residuals are large outliers; dropping a large fraction is itself flagged, since
it points at host copy-number change or a genotyping problem.</p>
{% endcall %}
{% endmacro %}

{# Collapsed "run command" provenance block. Single-sourced so the HTML footer
   and the PDF appendix render it identically. #}
{% macro run_command(params) %}
{% if params.command %}
<details class="run-command"><summary>Run command</summary><pre>{{ params.command }}</pre></details>
{% endif %}
{% endmacro %}

{# One headline figure card (label, big value, optional CI line). #}
{% macro figure_card(label, value, ci_str="") %}
<div class="figure-card">
<div class="figure-label">{{ label }}</div>
<div class="figure-value">{{ value }}</div>
<div class="figure-ci">{{ ci_str }}</div>
</div>
{% endmacro %}

{# Header identification band. `rows` is a list of (label, value) pairs. #}
{% macro header(rows) %}
<header class="header-band">
<h1>Chimerism report</h1>
<div class="meta-grid">
{% for label, value in rows %}
<div class="meta-item"><span class="meta-label">{{ label }}:</span><span class="meta-value">{{ value }}</span></div>
{% endfor %}
</div>
</header>
{% endmacro %}

{# Host-presence detection callout. `hp` is the detector sub-object (or none);
   `detected` is the precomputed verdict. Never silently omitted. `show_help`
   emits the inline "how it works" disclosure (HTML); the PDF sets it False and
   collects the same prose into its appendix. #}
{% macro host_presence(hp, detected, show_help=True) %}
<section class="section">
<h2>Host-presence detection</h2>
{% if hp is none %}
<div class="callout callout-neutral">
<div class="callout-title">Detection disabled</div>
<div>The dedicated host-presence detector was not run for this sample.</div>
</div>
{% elif (hp.n_markers or 0) == 0 %}
<div class="callout callout-neutral">
<div class="callout-title">Not assessable</div>
<div>No donor-homozygous markers were available to test for a host signal (artifact-filtered: {{ hp.n_artifact_filtered | count }}).</div>
</div>
{% else %}
<div class="callout {{ 'callout-amber' if detected else 'callout-neutral' }}">
<div class="callout-title">{{ 'Low-level host signal detected' if detected else 'No host signal above background' }}</div>
<div>Detection p-value (LRT): <strong>{{ hp.lrt_pval | pval }}</strong>; pooled-Poisson p-value: {{ hp.poisson_pval | pval }}.</div>
<div>Estimated host fraction: {{ hp.f_host_mle | pct(3) }} {{ ci(hp.f_host_ci_lo, hp.f_host_ci_hi) }}.</div>
<div class="small muted">Markers used: {{ hp.n_markers | count }}; error-rate source: {{ hp.error_rate_source }}; artifact-filtered: {{ hp.n_artifact_filtered | count }}.</div>
</div>
{% endif %}
{% if show_help %}{{ help_host_presence() }}{% endif %}
</section>
{% endmacro %}

{# A (Check, Value, Reference) metrics table. `rows` is a list of
   (label, value, reference) triples; value/reference are already safe text. #}
{% macro metrics(rows) %}
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
{% for label, value, ref in rows %}
<tr><td>{{ label }}</td><td class="num">{{ value }}</td><td class="muted small">{{ ref }}</td></tr>
{% endfor %}
</tbody>
</table>
{% endmacro %}

{# Quality-control panel. `ctx` carries the analysis dict, the two clinician
   summary lines, and the reference-threshold strings. `show_help` emits the
   inline "how it works" disclosure (HTML); the PDF sets it False and collects
   the same prose into its appendix. #}
{% macro qc_panel(ctx, show_help=True) %}
{% set a = ctx.analysis %}
{% set refs = ctx.refs %}
<section class="section">
<h2>Quality control</h2>
<div class="qc-verdict">Overall verdict: {{ badge(a.qc_status) }}</div>
<p class="qc-breakdown">{{ ctx.marker_accounting }}</p>
<p class="qc-breakdown">{{ ctx.flag_summary }}</p>

<h3 class="subhead">Markers</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
<tr><td>Total markers (input)</td><td class="num">{{ a.n_total_markers | count }}</td><td class="muted small"></td></tr>
<tr><td>Shared across samples</td><td class="num">{{ a.n_shared_markers | count }}</td><td class="muted small"></td></tr>
<tr><td>Informative</td><td class="num">{{ a.n_informative | count }}</td><td class="muted small"></td></tr>
<tr><td>Used in fit</td><td class="num">{{ a.n_used | count }}</td><td class="muted small"></td></tr>
{% if a.per_donor_n_informative %}
<tr><td>Informative per donor</td><td class="num">{% for n in a.per_donor_n_informative %}donor {{ loop.index }}: {{ n }}{{ ", " if not loop.last else "" }}{% endfor %}</td><td class="muted small"></td></tr>
{% endif %}
<tr><td>Excluded: low depth</td><td class="num">{{ a.n_excluded_depth | count }}</td><td class="muted small"></td></tr>
<tr><td>Excluded: quality</td><td class="num">{{ a.n_excluded_quality | count }}</td><td class="muted small"></td></tr>
<tr><td>Excluded: outlier</td><td class="num">{{ a.n_excluded_outlier | count }}</td><td class="muted small"></td></tr>
<tr><td>Robust refit dropped</td><td class="num">{{ (a.robust_drop_fraction or 0.0) | pct(0) }}</td><td class="muted small">{{ refs.robust }}</td></tr>
</tbody>
</table>

<h3 class="subhead">Sequencing depth (admixture)</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
<tr><td>Mean depth</td><td class="num">{{ a.mean_depth | num(0) }}x</td><td class="muted small">{{ refs.depth }}</td></tr>
<tr><td>Median depth</td><td class="num">{{ a.median_depth | num(0) }}x</td><td class="muted small"></td></tr>
<tr><td>Minimum depth</td><td class="num">{{ a.min_depth | count }}x</td><td class="muted small"></td></tr>
</tbody>
</table>

<h3 class="subhead">Model fit</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
<tr><td>Goodness-of-fit p</td><td class="num">{{ a.gof_pval | pval }}</td><td class="muted small">{{ refs.gof }}</td></tr>
{% if a.gof_pval_pretrim is not none %}
<tr><td>Goodness-of-fit p (pre-trim)</td><td class="num">{{ a.gof_pval_pretrim | pval }}</td><td class="muted small"></td></tr>
{% endif %}
</tbody>
</table>

<h3 class="subhead">Contamination</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
{% if a.contamination is none %}
<tr><td>Contamination</td><td class="num">not assessed</td><td class="muted small"></td></tr>
{% else %}
<tr><td>Contamination fraction</td><td class="num">{{ a.contamination.contamination_fraction | pct(3) }}</td><td class="muted small">{{ refs.contamination }}</td></tr>
<tr><td>Contamination p</td><td class="num">{{ a.contamination.p_value | pval }}</td><td class="muted small"></td></tr>
<tr><td>Contamination markers</td><td class="num">{{ a.contamination.n_markers | count }}</td><td class="muted small"></td></tr>
{% endif %}
</tbody>
</table>

<h3 class="subhead">Sample-swap</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
{% if a.admix_consistency is none %}
<tr><td>Sample-swap check</td><td class="num">not assessed</td><td class="muted small"></td></tr>
{% else %}
<tr><td>Swap discordant fraction</td><td class="num">{{ a.admix_consistency.discordant_fraction | pct(2) }}</td><td class="muted small"></td></tr>
<tr><td>Swap p</td><td class="num">{{ a.admix_consistency.swap_pval | pval }}</td><td class="muted small">{{ refs.swap }}</td></tr>
<tr><td>Consensus-homozygous markers</td><td class="num">{{ a.admix_consistency.n_consensus_hom | count }}</td><td class="muted small"></td></tr>
{% endif %}
</tbody>
</table>

<h3 class="subhead">Shared-het balance</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
{% if a.shared_het_balance is none or a.shared_het_balance.n_shared_het == 0 %}
<tr><td>Shared-het balance</td><td class="num">not assessed</td><td class="muted small"></td></tr>
{% else %}
<tr><td>Imbalanced fraction</td><td class="num">{{ a.shared_het_balance.imbalanced_fraction | pct(1) }}</td><td class="muted small">{{ refs.shared_het }}</td></tr>
<tr><td>Pooled VAF</td><td class="num">{{ a.shared_het_balance.pooled_vaf | num(3) }}</td><td class="muted small"></td></tr>
<tr><td>Shared-het markers</td><td class="num">{{ a.shared_het_balance.n_shared_het | count }}</td><td class="muted small"></td></tr>
{% endif %}
</tbody>
</table>

{% if a.run_unit is not none %}
{% set shares = a.run_unit.shares_run_with_host %}
<h3 class="subhead">Run provenance</h3>
<table class="metrics">
<thead><tr><th>Check</th><th class="num">Value</th><th>Reference</th></tr></thead>
<tbody>
<tr><td>Run unit</td><td class="num">{{ a.run_unit.run_unit if a.run_unit.run_unit else NA }}</td><td class="muted small"></td></tr>
<tr><td>Run-unit source</td><td class="num">{{ a.run_unit.source if a.run_unit.source else NA }}</td><td class="muted small"></td></tr>
<tr><td>Shares run with host</td><td class="num">{{ NA if shares is none else ("yes" if shares else "no") }}</td><td class="muted small">index-hopping risk if yes</td></tr>
</tbody>
</table>
{% endif %}

{% if a.relatedness %}
<h3 class="subhead">Reference-sample relatedness</h3>
<table class="metrics">
<thead><tr><th>Pair</th><th class="num">Coefficient</th><th class="num">95% CI</th><th>Relationship</th><th>Confidence</th><th class="num">Markers</th></tr></thead>
<tbody>
{% for r in a.relatedness %}
<tr><td>{{ r.a_name }} vs {{ r.b_name }}</td><td class="num">{{ r.coefficient | num(3) }}</td><td class="num">{{ ci(r.ci_low, r.ci_high, 3, as_pct=False) }}</td><td>{{ r.relationship }}</td><td>{{ r.confidence }}</td><td class="num">{{ r.n_sites | count }}</td></tr>
{% endfor %}
</tbody>
</table>
{% endif %}

{% if show_help %}{{ help_qc() }}{% endif %}

{% if a.warnings %}
<h3 class="subhead">Warnings</h3>
<ul class="warnings">
{% for w in a.warnings %}
<li>{{ w }}</li>
{% endfor %}
</ul>
{% else %}
<p class="muted small">No QC warnings raised.</p>
{% endif %}
</section>
{% endmacro %}

{# Methods / provenance footer. `show_run_command` emits the collapsed run-command
   block inline (HTML); the PDF sets it False and re-emits the same block in its
   "Methods and notes" appendix (browsers collapse <details>, so a printed report
   would otherwise hide it). #}
{% macro footer(version, params, citation, timestamp, show_run_command=True) %}
<footer class="footer section">
<h2>Methods and provenance</h2>
<dl>
<dt>allomix version</dt><dd>{{ version }}</dd>
<dt>Input files</dt><dd>{% if params.input_files %}{% for label, name in params.input_files %}{{ label }}: {{ name }}{{ "; " if not loop.last else "" }}{% endfor %}{% else %}{{ NA }}{% endif %}</dd>
{% for label, value in params.param_lines %}
<dt>{{ label }}</dt><dd>{{ value }}</dd>
{% endfor %}
<dt>Method</dt><dd>{{ citation }}</dd>
<dt>Report generated</dt><dd>{{ timestamp if timestamp else NA }}</dd>
</dl>
{% if show_run_command %}{{ run_command(params) }}{% endif %}
</footer>
{% endmacro %}