Add QC Comparison Table to Samples Panel

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Overview

Add a multi-sample QC comparison table to the top of the Samples panel, providing at-a-glance quality metrics for loaded samples.

Implementation Scope (MVP - Zero New Computation)

Location: Add to existing Samples panel (top section, above sample cards)

Data Source: Use only data already extracted during POD5/BAM load:

• From _squiggy_session.bam_info
• From _squiggy_session.pod5_path / read_ids
• No new Python computation required

UI Design: Comparison table showing side-by-side metrics

Metrics to Display

Metric	Source	Format
Basecaller Model	extract_model_provenance()	"dna_r10.4.1"
Basecaller Version	extract_model_provenance()	"guppy 5.0.0"
POD5 Reads	len(read_ids)	"14,234"
BAM Mapped	bam_info['num_reads']	"13,890"
Alignment Rate	Calculated	"97.6%"
References	len(bam_info['references'])	"12"
Modifications	bam_info['modification_types']	"5mC, 6mA" (formatted)
Has Events	bam_info['has_event_alignment']	✅/❌

Visual Design

╔════════════════════════════════════════════════════════════════╗
║ Samples                                                        ║
╠════════════════════════════════════════════════════════════════╣
║ QC COMPARISON (3 samples)                                      ║
║ ─────────────────────────────────────────────────────────────  ║
║ Metric              │ Sample A    │ Sample B    │ Sample C    ║
║ ────────────────────┼─────────────┼─────────────┼────────────  ║
║ Basecaller Model    │ dna_r10.4.1 │ dna_r10.4.1 │ rna004_70bps║
║ Basecaller Version  │ guppy 5.0.0 │ dorado 7.2  │ dorado 7.2  ║
║ POD5 Reads          │ 14,234      │ 14,234      │ 8,902       ║
║ BAM Mapped          │ 13,890      │ 14,102      │ 8,654       ║
║ Alignment Rate      │ 97.6%       │ 99.1% ✨    │ 97.2%       ║
║ References          │ 12          │ 12          │ 4           ║
║ Modifications       │ 5mC, 5hmC   │ 5mC, 6mA    │ Ψ, m7G      ║
║ Has Events          │ ✅          │ ✅          │ ✅          ║
║ ════════════════════════════════════════════════════════════   ║
║ MANAGE SAMPLES                                                 ║
║ Sample A                                        [👁️][▼]       ║
║   └─ [existing expandable card details]                       ║
║ Sample B                                        [👁️][▼]       ║
╚════════════════════════════════════════════════════════════════╝

Implementation Details

Backend (Python)

1. Add extract_model_provenance() call during BAM load if not already done
2. Store in bam_info['model_provenance'] = {name, version, basecaller}

Frontend (TypeScript/React)

1. Update squiggy-samples-core.tsx to add QC table section at top
2. Reuse existing modCodeToName mapping for modification display (from squiggy-modifications-core.tsx)
3. Calculate alignment rate: (bamReads / pod5Reads) * 100
4. Responsive table layout (collapses on narrow screens)

Message Passing

• QC data sent via existing updateSamples message
• No new message types needed

Behavior

Single Sample Mode:

• Show table with 1 column (still useful to see all metrics at once)

Multi-Sample Mode:

• Show comparison table with all samples side-by-side
• Highlight best values (e.g., highest alignment rate with ✨)

Collapsible:

• Add collapse/expand button to QC section
• Default: expanded (users want to see QC immediately)

Benefits

✅ Immediate value: Compare basecallers/models at a glance
✅ Zero cost: Uses only existing data
✅ No UI clutter: Fits in existing Samples panel
✅ Actionable: Quickly spot quality issues (low alignment, missing mods)

Future Enhancements (Out of Scope for MVP)

• Read length distribution (requires scanning all reads)
• Quality score distribution (requires BAM scan)
• Signal statistics (requires loading POD5 data)
• Interactive sorting/filtering of comparison table

Acceptance Criteria

• QC comparison table displays at top of Samples panel
• All 8 metrics shown correctly for each sample
• Modification types formatted with human-readable names
• Alignment rate calculated correctly
• Table responsive (works with 1-6+ samples)
• Collapsible section (default expanded)
• No performance impact on sample loading