v0.34.0 — Robustness & Infrastructure

v0.34.0 — Robustness & Infrastructure

Format Hardening (#75)

• Auto-detect plasmid file format via magic bytes (SnapGene vs xDNA vs GenBank vs FASTA)
• SnapGene .dna file support via BioPython parser
• Sanitized filename used as record ID (replaces truncated comment field)
• Actionable error messages for unsupported xDNA versions with conversion suggestions
• FASTA passthrough with sanitized record IDs

Output Restructuring (#80)

• OutputPaths frozen dataclass centralizes all path construction
• Organized subfolder layout: alignments/, references/, data/, reports/, plots/
• Depth-agnostic summary reader supports both old flat and new subfolder layouts
• All pipeline components use OutputPaths (no hardcoded path construction)

Cache Infrastructure (#39, #43)

• Content-addressed CacheManager at ~/.plasmicheck/cache/
• Within-run plasmid index deduplication
• Cross-run plasmid index caching with manifest (tool versions, input hashes)
• Cross-run spliced alignment caching (BAM, spliced reference, cDNA positions)
• CLI flags: --cache-dir, --no-cache
• Cache management subcommand: plasmicheck cache info|clean

Splice Junction Metadata (#68, Phase 1)

• Extract splice junction count and exon count from spliced alignment BAM CIGAR
• 11-field cDNA_positions.txt format with junction/exon/strand/chromosome metadata
• InsertRegionData dataclass with backward-compatible tuple unpacking
• Junction metadata displayed in per-sample and multi-sample reports
• TSV/Excel exports include junction metadata tables

Summary Visualization (#51)

• Verdict bar chart grouped by plasmid in summary reports
• Verdict bar chart grouped by sample in summary reports
• Matplotlib fallback for both new verdict bar charts
• Side-by-side Verdict Overview section in summary HTML template

Bug Fixes

• Fix pandas 2.2+ StringDtype compatibility on Python 3.12 (assign() vs .loc[])
• Fix temp file leak when plasmid conversion fails (try/finally cleanup)
• Fix NA cDNA positions creating bogus (0,0) insert region that misclassifies reads as Backbone_Only

Stats

• 20 requirements delivered across 5 phases (11 plans)
• 417 tests passing (120+ new tests)
• All CI checks green (lint, typecheck, Python 3.10 + 3.12)