Snapatac2

Features:

- Return more QC metrics from `pp.make_fragment_file`.
- Also compute library-level TSSe in `metrics.tsse`.
- `pp.make_fragment_file` can now work with 10X BAM files by specifying `source=10x`.
- Add `pp.call_cells` to identify nonempty barcodes from raw data.
- Add `pp.recipe_10x_metrics` to compute 10X metrics.
- Add `pp.import_contacts` to process scHi-C data.
- Implement pseudo-bulk peak calling in `tl.macs3`.

Other Changes:

- Change the default counting strategy from "insertion" to "paired-insertion" in
`pp.add_tile_matrix`, `pp.make_peak_matrix`, `pp.make_gene_matrix`.
- Minor changes in TSSe calculation.

Features:

- Implement 304: Add some flexibility to `pp.make_gene_matrix` by allowing the user to change
upstream and downstream distances for TSS calculation.
- Other minor improvements.

Bugs fixed:

- Fixed external sorter issues in version 2.6.2.

Features:

- Add the argument `exclude_chroms` to `metrics.tsse` to exclude certains chromosomes
from TSSe calculation. The default is "chrM".

Features:

- Add the argument `inplace` to AnnData `subset` function. As a result, if you
want to perform out-of-place subset, you need to set `inplace=False` explicitly.
Before you just need to set the `out` parameter. The benefit of this change
is that you can save the subset in memory by setting `out=None, inplace=False`,
which cannot be achieved before.
- Use only the unique TSSs instead of all TSSs read from the GTF file in `metrics.tsse` calculation.

Bugs fixed:

- Fix 252: `tl.spectral` does not raise an error when the input matrix is in
compressed column format, whereas it should expect a compressed sparse row format.
- Fix a bug in `pp.import_data` which produces incorrect duplication rates when
the input data contains mitochondrial reads.

Features:

- Add a argument `counting_strategy` to `pp.add_tile_matrix`, `pp.make_peak_matrix`, and `pp.make_gene_matrix`, which allows one to use different strategies
(insertion-based, fragment-based, or paired insertion counting) to compute feature counts.
- Fix 233: Add Apple silicon wheel files.

Bugs fixed:

- Fix 221: 'pp.knn' with 'method=pynndescent' invalid csr matrix.
- Fix 226: Backed AnnData does not support numpy string array.
- Fix 232: `tempdir` is not respected in `tl.macs3`.
- Fix 242: Change default value of `min_len` to `extsize` in `tl.macs3`, in order to be
consistent with the `macs3` command line tool.
- Other minor bug fixes.