Magenpy

Changed

- Fixed a bug in the phenotype likelihood inference in `SampleTable`.
- Changed the implementation of the `merge_snp_tables` utility function to
check for BOTH reference and alternative alleles.
- Modified implementation of `score` method of `GWADataLoader` to correct
potential issues with the BETAS being for a subset of the chromosomes.

Added

- A utility method to `GenotypeMatrix` called `estimate_memory_allocation`. This should
allow the user to gauge the memory resources required to interact with the
genotype files.

Changed

- Fixing bug in computing minor allele frequency with `plink`.

Added

- Added the reference allele `A2` to the list of attributes of `LDMatrix`.
- Added `effect_sign` as a property of `SumstatsTable`.

Changed

- Fixed implementation of `merge_snp_tables` to detect allele differences that
are not flips between `A1`/`A2`.
- Improved implementation of `.score` method of `xarrayGenotypeMatrix`.

Added

- Added `tqdm` progress bars when processing multiple files/chromosomes
in `GWADataLoader`.
- Added `min_maf` and `min_mac` flags in `magenpy_ld` and `magenpy_simulate`.

Changed

- Lowered default threshold for LD shrinkage to 1e-3.
- Bug fix in `SampleTable`.

Added

- Utility function to compute the genomic control or lambda factor.
- A method to set the causal SNPs directly in `GWASimulator`.

Changed

- Fixed bugs in `manhattan` plotting function.
- Added alternative ways to derive Chi-Squared statistic from
other summary stats (e.g. p-value).
- Give user more fine-grained control on what to reset in the `.simulate()`
method of `GWASimulator`.
- Modified the LD score computation method to allow for aggregating LD scores
by functional category or annotations.
- Streamlining module import structure to speed up loading.

Changed

- Fixed bugs in rechunking logic when computing LD matrices using `xarray`/`dask`