feat: support filtering of multi-allelic variants and loading of covariates in data/
#20
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note that this breaks links within the md files
feat: add md files to readthedocs
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NOTE: please merge #21 before this PR
see #19
This PR allows for filtering out multi-allelic variants in the Genotypes class. It also introduces a new Covariates class for reading covariate data. Unit tests for both features are also available.
There are also some small changes to our dependencies in pyproject.toml to resolve some conflicts between
clickandblack. Plus I changed the installation instructions to make sure everyone's using python 3.7I added a warning for cases where the Genotypes class loads 0 variants when the regions spec has the wrong 'chr' prefix. (This was an issue for me previously that I spent too much time debugging 😓)
I also added an
iterate()function to each class in the data moduleAnd I rewrote parts of the Genotypes.read() function to handle large datasets
Lastly, I double-checked that various inputs (stdin and gz files, mostly) are supported in the Phenotypes and Covariates classes.