Somaticseq

Use pybedtools instead of bedtools cli interface to call bedtools.
Plus some code and documentation maintenance.

Accepts complex variants from VCF files but convert them into snvs and indels.

Bug fix
- Fixed a misplaced `,` that broke the `--help` function in `somaticseq_run_workflows`. The script was still functional but the `--help` message could not print.
- Fixed links in README due to `example` moving to `tests/example`.

Mostly for maintenance
- Add `pyproject.toml` to modernize build scripts for `pip install .` as `./setup.py install` is being deprecated by python.
- Additional entrypoints for scripts shown in `pyproject.toml`. Scripts in `setup.py` are kept to be backward-compatible to previous command line interface.
- Extra packages for development can be installed via `pip install '.[dev]'`.
- Add an initial test in `tests` and moved `example` there.
- Refactored some functions

Mostly maintenance
- A lot of coding stylistic changes to make things more modern and easier to maintain
- Enforce versioning for some dependencies in `setup.py`, including `python>=3.10`
- For XGBoost model, additionally output json file (i.e., decision trees)
- Updated some docker files for 3rd party tools
- remove `-d dbsnp.vcf.gz` parameter from tumor-only LoFreq command (that param is only meaningful for tumor-normal pair)

**Full Changelog**: https://github.com/bioinform/somaticseq/compare/v3.7.4...v3.8.0

ntree_limit is replaced with iteration_range in xgboost.predict in xgboost >=1.4. This release uses `iteration_range=(0, iterations)` instead of `ntree_limit=iterations`.