fastdfe -

Made cyvcf2 optional via [vcf], improved DFE plot labels, added ancestral misidentification support and unnormalized Watterson’s theta to Spectrum class.

- Python
Published by Sendrowski 9 months ago

fastdfe -

Support for passing alternative optimizer to BaseInference and JointInference.

- Python
Published by Sendrowski 11 months ago

fastdfe -

Allow for probabilistic polarization when parsing SFS by looking at ancestral allele probability VCF info tag. Allow the transition/transversion ratio in the K2SubstitutionModel to be fixed to the value observed in the data. Adjust LRTs to account for parameters near boundaries. Extend ExistingOutgroupFiltration so that number of missing outgroups can be specified. Add RandomStratification and ContigFiltration classes.

- Python
Published by Sendrowski 12 months ago

fastdfe -

Add simulation class for simulating SFS data with known DFE.

- Python
Published by Sendrowski about 1 year ago

fastdfe -

Update cyvcf2 dependency to fix broken wheel for Mac ARM (https://github.com/brentp/cyvcf2/issues/305). Fix minor problem with remote files when disabling file caching.

- Python
Published by Sendrowski over 1 year ago

fastdfe -

Implement serialization of maximum likelihood ancestral annotation to allow for later inspection of results. Improve ancestral allele info tag information for site where annotation was not possible.

- Python
Published by Sendrowski almost 2 years ago

fastdfe -

Lazy-load some modules to allow faster initial loading. Update docs.

- Python
Published by Sendrowski almost 2 years ago

fastdfe -

Draft release to receive a DOI on Zenodo.

- Python
Published by Sendrowski almost 2 years ago

fastdfe -

Allow for Python 3.12, improve documentation on installation process, pin Python to 3.11 when installing from R interface, exclude large files from distribution to speed up installation in R.

- Python
Published by Sendrowski almost 2 years ago

fastdfe - v1.1.4

Update docs and dependencies, and minor improvements.

- Python
Published by Sendrowski about 2 years ago

fastdfe -

Implement probabilistic subsampling for ancestral allele annotation and minor improvements.

- Python
Published by Sendrowski about 2 years ago

fastdfe - v1.1.2

Improve bootstrapping and set allow_divergence flag to false by default which as it has the potential to bias the SFS. Improve docs.

- Python
Published by Sendrowski over 2 years ago

fastdfe -

Probabilistic parsing of SFS, functionality to subsample already existing SFS to lower sample size. Support for number of target sites for ancestral allele annotation, improved parallelization when bootstrapping, new plotting functionalities, improved docs and logging and some minor improvements.

- Python
Published by Sendrowski over 2 years ago

fastdfe - v1.1.0

Improved parsing utilities, ancestral allele annotation with outgroups and plenty of minor improvements.

- Python
Published by Sendrowski over 2 years ago

fastdfe -

First stable release.

- Python
Published by Sendrowski over 2 years ago

fastdfe - New beta version.

- Python
Published by Sendrowski over 2 years ago

fastdfe - More stable beta release

- Python
Published by Sendrowski over 2 years ago

fastdfe - New pre-release

Bug fixes and addition of VCF annotation and filtration capabilities.

- Python
Published by Sendrowski almost 3 years ago

fastdfe -

Bug fixed and improvements.

- Python
Published by Sendrowski almost 3 years ago

fastdfe - New beta release

A lot of bugs fixed. The covariates should work now.

- Python
Published by Sendrowski almost 3 years ago

fastdfe - Beta release.

Beta release.

- Python
Published by Sendrowski almost 3 years ago