Breaking changes:
- Fragments are now stored in `.obms['fragment_single']` or `.obsm['fragment_paired']`, depending on whether the data is single-end or paired-end. As a result, the h5ad files generated prior to this version are no longer compatible.
- `tl.call_peaks` has been renamed to `tl.macs3`, and the underlying algorithm has been significantly improved, see 142. `tl.macs3` doesn't automatically merge returned peaks anymore. Use `tl.merge_peaks` to merge peaks. Please read the updated tutorial for more details.
- `pp.import_data` now doesn't compute the TSS enrichment scores. Use `metrics.tsse` to compute the TSS enrichment scores. `genome` parameter is renamed to `chrom_sizes`.
Features:
- Add `tl.merge_peaks` to perform peak merging.
- Allow using custom mitochondrial chromosome names in `pp.import_data`.
- Change the default algorithm in `pp.knn` to kd-tree.
Bugs fixed:
- 165: Fix reproducibility issues in various functions.