Celescope

Based on v1.5.1. Add support for chemistry scopeV3.0.1

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`.

Added

- Add `min_consensus_read` argument to `celescope.tools.consensus`. If
1. the percentage of the most common residue type > threshold;
2. most common residue reads >= min_consensus_read;

then we will add that residue type, otherwise an ambiguous character will be added.

Changed
- By default, use otsu method to calculate `min_support_read` for `capture_virus`.

- By default, use otsu method to calculate `min_support_read` for `snp`.

- Improved the code of `celescope.snp.variant_calling` to reduce memory usage and speed up analysis.

- Add serveral arguments in `vdj` and `tag` to support WDL workflow.

Fixed

- Fix a bug in `celescope.tag.count_tag` when there is no `Undetermined` cells.

- Fix a bug in `celescope.snp.variant_calling` when there are multiple variants at the same loci in a cell.

Added
Add dynascope assay.
Add celescope tag split_tag.
Changed
Change fastq file pattern of mapfile: Remove * before library_id.
celescope.tools.count_capture_virus: Change min_support_read from 1 to 2.
Fixed
celescope.tools.count will report an error when there are multiple gtf or refFlat file under genomeDir.
Removed
celescope.tools.utils.glob_genomeDir