Celescope

`rna` and `dynaseq`
- Fix an issue that mitochondrial percent is not added to metrics.

`snp`,`capture_virus` and `fusion`
- When calculating the `auto` threshold, the default coefficient changes from 10 to 3. This will make the filtering more stringent.

General improvments
- Fix an issue where the matrix suffix `filtered_feature_bc_matrix` introduced in v1.8.0 is not recognized when parsing match_dir.

`rna` and `dynaseq`
- Replace `Seurat` with `scanpy`.
- Add read_saturation to downsample file.

`snp`,`capture_virus` and `fusion`
- When calculating `otsu` threshold, use `math.ceil` instead of `int`.

General improvments
- Fix an issue where the conditions for detecting scopeV2.0.1 are too loose. (108)
- Move `sjm.job` from `./log/` to `./sjm/`.
- Change output file suffix.
- raw_matrix: `all_matrix` -> `raw_feature_bc_matrix`
- fitered_matrix: `matrix_10X`-> `filtered_feature_bc_matrix`

`vdj`
- "Cell with Barcode Match, TRA and TRB": When calculating the percentage, the denominator is `Cell with Barcode Match`. The denominator used previously was `Estimated Mumber of Cells`.

`capture_virus` and `fusion`
- Make UMI correction optional. If you do not want to perform UMI correction, use `--not_correct_UMI`.
- Add a filtering step to filter UMI with supporting reads less then read_threshold.

`dyanseq`
- modify vcf base [96](https://github.com/singleron-RD/CeleScope/pull/96).

General improvments
- Remove the redundant `--assay` parameter.
- Add the `--queue` argument for `sjm` job submission.

`rna`
- Fix a bug with mt_gene_list (92)

`snp`
- Add a fitering step: `celescope snp filter_snp` with arguments `--threshold_method`. Choices can be one of
- `auto` : Default method. Using a method similar to cell calling method.
- `otsu` : Counts are first log transformed and then the threshold is determined by [Otsu's method](https://en.wikipedia.org/wiki/Otsu%27s_method).
- `hard` : Using user provided UMI threshold.
- `none` : Do not perform filtering.

`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.