Celescope

`capture_virus`
- Add documents.
- Add UMI filtering options - 'auto'.
- Add UMI correction.
- Extract the filtering process into a separate step.
- Remove the `otsu` choice from `--min_support_read`.

`tag`
- Remove `--marker_file` argument from `analysis_tag`.

General improvments
- Optimize the display of t-SNE plots in HTML reports.

`snp`
- Increase `max-depth` from 1M to 100M to avoid calculation errors at very deep sites.

General improvments
- Fix a bug that `featureCounts` didn't output name sorted bam file.
- Fix a bug that `Median Enriched Reads per Valid Cell` in `target_metrics` used all cell number as denominator, not valid cell number.
- Fix a problem that the Q30 metrics in the html report showed too much precision.

`snp`
- Improve the speed and memory usage.
- Format the output files to avoid redundant information.
- Fix an issue that the number of cells of each genotypes were not calculated correctly.
- Remove `CID` and `VID` in all the output files.

General improvments
- Improve the speed of `add_tag`.
- Remove support for deprecated cell-calling method `inflection`.

General improvments
- Add auto-detection for chemistry `scopeV3.0.1`.
- Remove support for deprecated chemistry `scopeV2.0.0` and `scopeV2.1.0`.

`snp`
- Add `--panel` option.
- Add output files.
- Improve the speed of `variant_calling`.


`fusion`
- Fix a bug where `celescope.fusion.count_fusion` do not recognize fusion reads correctly.

`dynascope`
- Fix some bugs (62).

General improvments
- Use local css instead of urls to avoid connection issues.

Added

- Add `--split_vdj` in `celescope.tag.split_tag` to split vdj library according to tag assignment.
- Add Docs for `snp`.

Changed

- `snp.variant_calling` change `--do-not-fix-overhangs` from `false` to `true` to avoid omitting variants in the overhang region.

Fixed

- Fix a memory leak in `snp.variant_calling`.

Removed