Magenpy

Changed

- Fixed `manhattan` plot implementation to support various new features.
- Added a warning when accessing `csr_matrix` property of `LDMatrix` when it hasn't been loaded
previously.

Added

- `reset_mask` method for magenpy `LDMatrix`.
- `Dockerfile`s for both `cli` and `jupyter` modes.
- A helper script to convert LD matrices from old format to new format.

Changed

- Fixed bugs in how covariates are processed in `SampleTable`.
- Fixed bugs / issues in implementation of GWAS with `xarray` backend.
- Streamlined implementation of `manhattan` plotting function.

A large scale restructuring of the code base to improve efficiency and usability.

Changed

- Bug fixes across the entire code base.
- Simulator classes have been renamed from `GWASimulator` to `PhenotypeSimulator`.
- Moved plotting script to its own separate module.
- Updated some method names / commandline flags to be consistent throughout.

Added

- Basic integration testing with `pytest` and GitHub workflows.
- Documentation for the entire package using `mkdocs`.
- Integration testing / automating building with GitHub workflows.
- New implementation of the LD matrix that uses CSR matrix data structures.
- Quantization / float precision specification when storing LD matrices.
- Allow user to specify Compressor / Compressor options for Zarr storage.
- New implementation of `magenpy_simulate` script.
- Allow users to set random seed.
- Now accept `--prop-causal` instead of specifying full mixing proportions.
- Tried to incorporate `genome_build` into various data structures. This will be useful in the
future to ensure consistent genome builds across different data types.
- Allow user to pass various metadata to `magenpy_ld` to save information about dataset
characteristics.
- New sumstats parsers:
- Saige sumstats format.
- plink1.9 sumstats format.
- GWAS Catalog sumstats format.
- Chained transform function for transforming phenotypes.

Changed

- Removed the `--fast-math` compiler flag due to concerns about
numerical precision (e.g. [Beware of fast-math](https://simonbyrne.github.io/notes/fastmath/)).
- Updated implementation of `SumstatsParser` class to allow user to specify `read_csv_kwargs` at the point of instantiation.
- Updated plink executors to propagate the error messages to the user.
- Updated `merge_snp_tables` to allow for merges on columns other than `SNP`.
- Refactored, cleaned, and updated the implementation of the `AnnotationMatrix` class.
- Fixed bug in `GWADataLoader.split_by_samples()`: Need to perform `deepcopy`, otherwise splitting would not work properly.
- Updated `read_annotations` method in `GWADataLoader` to work with the latest `AnnotationMatrix` interfaces.
- Fixed bug in the `manhattan` plotting function.

Added

- Added parsers for functional annotations and annotation files. Mainly support LDSC annotation format for now.
- Added a utility method to `GWADataLoader` called `align_with` to streamline aligning `GWADataLoader` objects across SNP and sample dimensions.
- Added utility methods for flattening the LD matrix in `LDMatrix`.
- Added a method to perform matrix-vector multiplication in `LDMatrix`.
- Added a method to perform block-wise iteration in the `LDMatrix` class.

Changed

- Fixed bug in implementation of `identify_mismatched_snps`.
- Fixed bugs in handling of missing information in LD matrix.
- Fixed bug in handling of covariates in `SampleTable`.
- Updated `README` file to remove line indicators `>>>` from sample code.

Added

- Added the reference allele `A2` to the output of the `true_beta_table`
in `GWASimulator`.

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.