Changelog

Explanations of major changes to vcfsim are listed below. For up-to-date info on minor versions and bugfixes, see the release notes on GitHub: https://github.com/samuk-lab/vcfsim/releases

Unreleased

Documentation

  • Added Sphinx documentation hosted on Read the Docs.

vcfsim 1.0.29

New features

  • Comma-separated samples. --samples and --samples_file now accept either comma- or whitespace-separated names, so the same list can be pasted into either flag.

  • Two-population mode (--population_mode 2) for simulating a clean C → A, B split at a user-specified divergence time (--div_time).

  • HMM-based site missingness. Four new flags (--hmm_baseline, --hmm_multiplier, --hmm_p_low_to_high, --hmm_p_high_to_low) produce spatially clustered missingness instead of the uniform --percent_missing_sites pattern.

Bug fixes

  • Several VCF formatting fixes for downstream compatibility.

Packaging

  • Refactored VCF generation; bumped version and dependencies.