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Changelog

All notable changes to MucOneUp will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Fixed

  • ONT amplicon pipeline now reads from dedicated ont_amplicon_params config section instead of pacbio_params -- was using PacBio Sequel model (ERRHMM-SEQUEL) for ONT reads (#79)
  • CLI routes --model-file overrides to ont_amplicon_params for ONT and pacbio_params for PacBio

Added

  • ont_amplicon_params config section with ONT-specific defaults (QSHMM-ONT-HQ.model)
  • OntAmpliconConfig TypedDict for type-safe ONT parameter access
  • Config schema validation and path resolution for ont_amplicon_params
  • Test for ONT platform using ont_amplicon_params (not pacbio_params)
  • Documentation: ONT configuration section in amplicon simulation guide

[0.43.4] - 2026-04-06

Fixed

  • Race condition in VNTR efficiency temp directory — replaced deterministic path with tempfile.TemporaryDirectory for process-safe isolation in parallel runs (#82)

[0.43.3] - 2026-04-06

Fixed

  • ONT amplicon: warn when model file does not appear to be an ONT model (#79)
  • pbsim3 wrapper: detect and convert numbered SAM files (prefix_0001.sam) produced with template mode (#79)
  • Config paths (model_file, reseq_model, human_reference) now resolved relative to config file directory, not working directory (#80)
  • Default expected_product_range widened from [1500, 6000] to [1500, 15000] to support VNTRs with >99 repeats (#81)

Added

  • 5 new tests for config path resolution, ONT model warning, and numbered SAM detection

[0.43.2] - 2026-04-06

Added

  • --read-number CLI option for reads illumina to control fragment generation count
  • 3 new CLI tests for --read-number option

Changed

  • Default read_number raised from 10,000 to 100,000 in config.json (was limited by original ReSeq deadlock bug, now resolved by ReSeq2)

[0.43.1] - 2026-04-05

Changed

  • Replaced ReSeq with ReSeq2 as the recommended Illumina error modeling tool
  • Removed seqToIllumina timeout workaround — ReSeq2 v2.0.3 fixes the upstream deadlock bug that limited the original ReSeq to ~10,000 reads
  • Default seqToIllumina timeout raised from 120s to 600s (safety net only)

Removed

  • seqtoillumina_timeout config parameter (no longer needed)

[0.43.0] - 2026-04-05

Added

  • ONT amplicon simulation via reads amplicon --platform ont
  • --platform option for reads amplicon command (choices: pacbio, ont)
  • Shared amplicon preparation module (amplicon_common.py) used by both platforms
  • Assay_type field in simulation metadata TSV
  • assay_type and ont-amplicon to config schema
  • keep_intermediate_files support in ONT amplicon pipeline
  • 13 new tests for ONT amplicon pipeline, shared helpers, CLI routing, and metadata

Changed

  • Relaxed pbsim3 pass_num validation from >= 2 to >= 1 (ONT single-pass)
  • Refactored PacBio amplicon pipeline to use shared extraction stages
  • Metadata platform field changed from PacBio-Amplicon to PacBio with separate assay_type

0.40.0 - 2026-04-04

Added

  • PacBio amplicon read simulation using PBSIM3 template mode (reads amplicon command)
  • PCR length bias model with exponential decay, calibrated to Madritsch et al. 2026 empirical data
  • Deterministic and stochastic (Galton-Watson) PCR bias modes
  • Preset profiles (default, no_bias) for PCR bias configuration
  • Primer-based amplicon extraction from diploid VNTR references
  • Shared primer binding site utility (refactored from snapshot validator)
  • amplicon_params configuration section with primer sequences and PCR bias settings
  • 69 new tests covering all amplicon simulation components

Changed

  • Updated GitHub Actions to Node.js 24 compatible versions (checkout v6, setup-python v6, setup-uv v7)
  • Extended config schema to accept "amplicon" and "pacbio" as simulator types

0.19.0 - 2025-10-20

Added

  • MkDocs Material documentation system with GitHub Actions deployment
  • Comprehensive user guides (simulation, toxic protein detection, SNaPshot validation)
  • Auto-generated CLI documentation via mkdocs-click
  • Dark/light mode toggle, instant search, mobile responsive design
  • Professional documentation at https://berntpopp.github.io/MucOneUp/

0.15.0 - 2025-10-18

Added

  • In silico SNaPshot assay validation for MUC1 dupC mutation

0.14.0 - 2025-10-15

Added

  • Diploid split-simulation for ONT reads

Fixed

  • ONT read simulation bias in diploid references

0.13.0 - 2025-10-10

Added

  • Toxic protein detection algorithm
  • ORF prediction with orfipy integration

Earlier Versions

See GitHub Releases for earlier version history.