Sniffles

manage the Sniffles2Exit exception in order to not have `--version` and `--help` trowing an exit code 1 which made conda not accept sniffles v2.3.1

**Full Changelog**: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3.1...v2.3.2

**Bug fixes** that prevented pip installation to work and thus conda was unable to build and release
**Full Changelog**: https://github.com/fritzsedlazeck/Sniffles/compare/v2.3...v2.3.1

This release includes new features for multisample calling and some restructuring of the codebase to facilitate easier development in the future.

New features:

- Multisample calling for large input sets
Sniffles multiprocessing code has undergone a major rewrite with focus of enabling multisample calling for a large number of input files. To support this, the new optional dependency _psutil_ can be installed along with sniffles.

- Using alignments for multisample calling
Alignments can be used to improve separation of variants in multisample calling. This uses the new optional dependency _edlib_ and can be tweaked with the new argument `--combine-pctseq` defaulting to 0.7.

Required Python version has been updated to Python 3.10.

This release includes a number of updated implementation, bug fixes and usability improvements.

- Low frequency SV caller mode `--non-germline` has been updated to `--mosaic `
- Sniffles now allow SV on the same breakpoint
- Minimum SV length is updated to 50 bases
- Minimum mapping quality is set to 20 as default
- Translocation events: require a minimum anchor on each chromosome of 1kb and there a strand check (`--bnd-min-split-length` and --qc-`bnd-filter-strand`)
- We include a link to a Sniffles2 plotting tools: [https://github.com/farhangus/sniffle2_plot](https://github.com/farhangus/sniffle2_plot)

This release includes a number of minor bugfixes and usability improvements.

- Create output directories if they are not existing yet (wdecoster)
- Change --max-splits-kb to float (wdecoster)
- Fixed a problem where exit code 0 was returned on errors

In comparison to 2.0.2 a number of improvements to multi-sample mode were added:

* Improved choice of insertion sequence for reporting
* Added additional INFO fields to multi-sample output
* Fixed a problem causing inconsistent start/end coordinates for deletions
* Increased strictness of default merging parameters