Jerome Kelleher
Jerome Kelleher
In our docs for Fst we provide the formula for how it's computed, but don't explain which version of Fst this corresponds to. Is this one of the estimators (Hudson/Weir...
#1825 added support for alignments, which passed through arguments for supporting missing data to the haplotypes method. However, the initial implementation was wrong. Consider the following example: ```python # 2.00┊...
It feels like it would clarify things for most users, and help with search engine visibility. Thoughts?
I've spent the day tracking down a bug in sc2ts, which is pointing towards being a problem with tsinfer's multi-allele handling (and allele index rotating to deal with non-zero ancestral...
https://github.com/tskit-dev/msprime/issues/1485 Best to workaround with a pin for now, but will need a more complete solution.
It would be useful to automatically remove bits of the tree sequence that we think are suspect quality. This would remove all sites within the mask from inference and afterwards...
The C code assertions require that nodes cannot be marked as both samples and synthetic.
Add fixed with formats to the progress bar format so that it looks like what's shown in the tutorial.
See https://github.com/sgkit-dev/bio2zarr/issues/391 for details. It's less obviously incorrect here than in bio2zarr where we're striving for compatability, but it's still a surprising choice which should be documented if there's a...
Here's my code: ``` data_path = "tests/data/plink/" bed_path = data_path + "plink_sim_10s_100v_10pmiss.bed" fam_path = data_path + "plink_sim_10s_100v_10pmiss.fam" bim_path = data_path + "plink_sim_10s_100v_10pmiss.bim" # print(bed_path) # print(fam_path) sg_ds = sgkit.io.plink.read_plink( bed_path=bed_path,...