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Integration with scikit-allel: SFS and joint SFS calculations - #71
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`grapp.popgen` now supports extracting allele count output that is directly compatible with many scikit-allel popgen functions. Specifically, we can now extract per-population allele counts, and extract the ref/alt allele counts in a matrix form that can be passed directly to scikit-allel's folded SFS functionality. `grapp.popgen.sfs` also contains wrappers around scikit-allel that will compute SFS information for all population pairs, e.g. for extracting the joint SFS information for demographic inference. This functionality is still a work in progress, and APIs may change. The f-statistics (both classical and admixture ones) from scikit-allel should also be compatible with `grapp.popgen`, and at some point I will add wrappers for those as well.
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grapp.popgennow supports extracting allele count output that is directly compatible with many scikit-allel popgen functions. Specifically, we can now extract per-population allele counts, and extract the ref/alt allele counts in a matrix form that can be passed directly to scikit-allel's folded SFS functionality.grapp.popgen.sfsalso contains wrappers around scikit-allel that will compute SFS information for all population pairs, e.g. for extracting the joint SFS information for demographic inference.This functionality is still a work in progress, and APIs may change. The f-statistics (both classical and admixture ones) from scikit-allel should also be compatible with
grapp.popgen, and at some point I will add wrappers for those as well.