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Genome Forge v0.1.16

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@felizvida felizvida released this 15 Jun 19:41
· 1 commit to master since this release
v0.1.16
f2b5682

Genome Forge v0.1.16

This release adds the first NGS-lite replacement-phase workflow: FASTQ QC, adapter/quality trimming, lightweight read mapping, simple variant evidence, and a one-click workflow report for small amplicon or construct-verification read sets.

Highlights

  • Added POST /api/fastq-qc for read counts, length distribution, GC, Q20/Q30, per-base quality, and adapter detection.
  • Added POST /api/fastq-trim for deterministic adapter and quality trimming with retained/dropped read audit rows.
  • Added POST /api/ngs-map-reads for local read-to-reference mapping, coverage, consensus, zero-coverage regions, read-level mapping rows, and high-support variant evidence.
  • Added POST /api/ngs-workflow-report for QC -> trimming -> mapping -> expected/unexpected variant checks and replacement-phase status.
  • Added an NGS Lite browser tab and evidence report panel.
  • Expanded the self-study book to 46 cases with Case AT, "NGS-Lite Amplicon Evidence Report."

Validation

  • make quality PYTHON=./.venv-docs/bin/python3
  • ./.venv-docs/bin/python3 -m unittest discover -s tests -p 'test_*.py'
  • ./.venv-docs/bin/python3 smoke_test.py
  • ./.venv-docs/bin/python3 real_world_functional_test.py
  • npm run test:e2e
  • git diff --check

Baseline

  • Unit tests: 57/57
  • Smoke checks: 119/119
  • Real-world workflow steps: 110/110
  • Browser E2E tests: 16/16
  • API inventory: 118 documented /api/* endpoints plus GET /share/<share_id>
Assets 5
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