[0.2.0] - 2022-11-01

Major feature release adding many new species and models, as well as support for simulating selection via SLiM.

Bug fixes:

  • Parameters in the HomSap/Zigzag_1S14 model now match those in Schiffels & Durbin (2014) (@grahamgower, #750).

  • Recombination rate for DroMel chr4 changed to 0 (@izabelcavassim, #1092).

  • Per-chromosome mean recombination rates for HomSap were incorrectly calculated (@nspope, #1345).

Breaking changes:

  • Removed GeneticMap class from public API (@jeromekelleher, #713).

  • Samples are now specified via population/individual pairs, using species/chromosome ploidy. The old API for specifying haploid samples via population index has been retained, but is deprecated and will be removed at some point (@nspope, #1361).

New species:

New models:

New genetic maps:

New features:

Additions to CLI:

  • Sample specification has switched from positional and haploid (e.g. stdpopsim HomSap -d OutOfAfrica_3G09 6 0 10) to named with species-specific ploidy (equivalent to stdpopsim HomSap -d OutOfAfrica_3G09 YRI:3 CEU:0 CHB:5). Positional sample specification is still supported but will raise a deprecation warning.

  • Arguments --dfe, --dfe-interval, --dfe-bed-file, --help-dfe for specifying DFEs (@izabelcavassim, #1052).

  • Arguments --help-annotations, --dfe-annotation for associating annotation tracks with DFEs (@andrewkern, #1117).

  • Argument --length for simulating from a generic contig (@apragsdale, #664).

  • Arguments --inclusion-mask, --exclusion-mask for masking simulated sequences (@apragsdale, #664).

  • Arguments --left and --right for simulating an interval on a named chromosome (@nspope, #1348)

  • Argument --keep-mutation-ids-as-alleles retains SLiM mutation IDs for allele codes instead of converting these to nucleotides (@nspope, #1356).

Catalog maintenance infrastructure:

New annotations:

New DFEs:

[0.1.2] - 2020-05-29

Important bugfix and feature release, recommended for all users.

Significant errors in the HomSap/OutOfAfrica_3G09 and HomSap/OutOfAfrica_2T12 models have been fixed. We recommend repeating any analyses performed using these models. See here for more details on the error in the three population Out of Africa model and analysis of the differences from the correct model.

The recombination rate for AraTha was also off by a factor of 10. We recommend repeating any analyses performed using this species.

Bug fixes:

  • Fix error in HomSap/OutOfAfrica_3G09 model, in which migration between ancestral African and European populations was allowed to continue in the most ancient time period (@apragsdale, #496, #516).

  • Fix similar error in HomSap/OutOfAfrica_2T12 model (@ndukler, #520, #516).

  • Fix recombination rate estimate for AraTha (@grahamgower, #537, #527), which was off by a factor of 10.

  • Require attrs >=19.10 (@grahamgower, #399, #394)

New species:

New models:

New features:

Breaking changes:

  • Move the –quiet/-q command line option to the top-level. Previously we would write stdpopsim HomSap -q 10 whereas we now write stdpopsim -q HomSap. (@jeromekelleher, #515, #547)

  • The long form --verbosity argument has been changed to --verbose (#547).

  • Removed DroMel chrM (@grahamgower, #528, #405).

[0.1.1] - 2020-01-02

Bugfix release. Fixes some distribution issues and temporarily removes the PonPyg species.

Bug fixes:

New features:

Breaking changes:

  • Temporarily remove the PonPyg species from the catalog to provide time to fix issues with genomes and multi-species models (#365).

[0.1.0] - 2019-12-18

Initial release.