Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

web/src/routes/+layout.svelte

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+<script lang="ts">
+  import '../app.css';
+  let { children } = $props();
+</script>
+
+<main>{@render children()}</main>

web/src/routes/+page.svelte

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+<script lang="ts">
+  import { onMount } from 'svelte';
+  import { api, type Sample } from '$lib/api';
+
+  let samples = $state<Sample[]>([]);
+  let name = $state('');
+  let vcfUri = $state('');
+  let error = $state<string | null>(null);
+
+  async function refresh() { samples = await api.samples(); }
+  onMount(refresh);
+
+  async function add() {
+    error = null;
+    try { await api.createSample({ name, vcf_uri: vcfUri }); name = ''; vcfUri = ''; await refresh(); }
+    catch (e) { error = (e as Error).message; }
+  }
+</script>
+
+<h1>rarelens</h1>
+<p class="lede">Annotate a VCF with Ensembl VEP, score each variant, and browse what came back. Public test data only.</p>
+
+<h2>Add a sample</h2>
+<div style="display:flex; gap:0.5rem; flex-wrap:wrap">
+  <input placeholder="Sample name" bind:value={name} aria-label="Sample name" />
+  <input placeholder="gs://bucket/sample.vcf.gz or /data/example.vcf.gz" bind:value={vcfUri} aria-label="VCF path" style="flex:1; min-width: 20rem" />
+  <button onclick={add} disabled={!name || !vcfUri}>Add sample</button>
+</div>
+{#if error}<p role="alert">Could not add the sample: {error}</p>{/if}
+
+<h2>Samples</h2>
+{#if samples.length === 0}
+  <div class="empty">No samples yet. Add one above to run the annotation pipeline.</div>
+{:else}
+  <table>
+    <thead><tr><th>Name</th><th>VCF</th><th>Assembly</th><th>Added</th></tr></thead>
+    <tbody>
+      {#each samples as s (s.id)}
+        <tr>
+          <td><a href="/samples/{s.id}">{s.name}</a></td>
+          <td class="hgvs">{s.vcf_uri}</td>
+          <td>{s.assembly}</td>
+          <td>{new Date(s.created_at).toLocaleDateString('en-GB')}</td>
+        </tr>
+      {/each}
+    </tbody>
+  </table>
+{/if}

web/src/routes/samples/[id]/+page.svelte

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+<script lang="ts">
+  import { onMount } from 'svelte';
+  import { api, type Job, type VariantPage } from '$lib/api';
+
+  let { data } = $props();
+  let job = $state<Job | null>(null);
+  let page = $state<VariantPage | null>(null);
+  let gene = $state('');
+  let impact = $state('');
+  let maxAf = $state('0.01');
+  let busy = $state(false);
+
+  onMount(async () => {
+    const jobs = await api.jobsForSample(data.sampleId);
+    const done = jobs.find(j => j.status === 'succeeded');
+    if (done) { job = done; await loadVariants(); }
+    else if (jobs.length) job = jobs[0];
+  });
+
+  async function runAnnotation() {
+    busy = true;
+    job = await api.annotate(data.sampleId);
+    const poll = setInterval(async () => {
+      if (!job) return;
+      job = await api.job(job.id);
+      if (job.status === 'succeeded' || job.status === 'failed') { clearInterval(poll); busy = false; if (job.status === 'succeeded') await loadVariants(); }
+    }, 3000);
+  }
+
+  async function loadVariants() {
+    if (!job) return;
+    const q: Record<string, string> = { job_id: job.id, max_af: maxAf, limit: '100' };
+    if (gene) q.gene = gene;
+    if (impact) q.impact = impact;
+    page = await api.variants(q);
+  }
+
+  const scoreClass = (s: number) => (s >= 0.8 ? 'score high' : s >= 0.5 ? 'score mid' : 'score');
+</script>
+
+<a href="/">All samples</a>
+<h1>Sample {data.sampleId.slice(0, 8)}</h1>
+
+{#if !job}
+  <button onclick={runAnnotation} disabled={busy}>Run VEP annotation</button>
+{:else}
+  <p>Job <span class="hgvs">{job.id.slice(0, 8)}</span>: <span class="status {job.status}">{job.status}</span></p>
+{/if}
+
+{#if job?.status === 'succeeded'}
+  <h2>Variants</h2>
+  <div style="display:flex; gap:0.5rem; flex-wrap:wrap; margin-bottom:0.75rem">
+    <input placeholder="Gene symbol" bind:value={gene} aria-label="Gene" />
+    <select bind:value={impact} aria-label="Impact">
+      <option value="">Any impact</option><option>HIGH</option><option>MODERATE</option><option>LOW</option><option>MODIFIER</option>
+    </select>
+    <label>Max gnomAD AF <input type="number" step="0.001" min="0" max="1" bind:value={maxAf} style="width:6rem" /></label>
+    <button class="quiet" onclick={loadVariants}>Apply filters</button>
+  </div>
+
+  {#if page && page.items.length === 0}
+    <div class="empty">No variants match these filters. Raise the allele frequency cap or clear the gene filter.</div>
+  {:else if page}
+    <p style="color:var(--ink-soft)">{page.total} variants, showing {page.items.length}</p>
+    <table>
+      <thead><tr><th>Position</th><th>Gene</th><th>Consequence</th><th>HGVS</th><th>gnomAD AF</th><th>ClinVar</th><th>Score</th></tr></thead>
+      <tbody>
+        {#each page.items as v (v.id)}
+          <tr>
+            <td class="coord">{v.chrom}:{v.pos} {v.ref}>{v.alt}</td>
+            <td>{v.gene ?? ''}</td>
+            <td>{v.consequence ?? ''}<br /><small style="color:var(--ink-soft)">{v.impact ?? ''}</small></td>
+            <td class="hgvs">{v.hgvsp ?? v.hgvsc ?? ''}</td>
+            <td>{v.gnomad_af?.toExponential(2) ?? 'absent'}</td>
+            <td>{v.clinvar_sig ?? ''}</td>
+            <td>{#if v.prediction}<span class={scoreClass(v.prediction.score)}>{v.prediction.score.toFixed(2)}</span>{:else}<span style="color:var(--ink-soft)">unscored</span>{/if}</td>
+          </tr>
+        {/each}
+      </tbody>
+    </table>
+  {/if}
+{/if}

web/src/routes/samples/[id]/+page.ts

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+import type { PageLoad } from './$types';
+export const load: PageLoad = ({ params }) => ({ sampleId: params.id });