Addition of spacer mapping

See merge request SRoux/spacerextractor!2

Add the possibility for users to adjust denoising level, and improve look of help message for individual commands

First commit with the addition of spacer mapping - still need to add the auto-detection of target-encoded arrays

Bump to 0.9.3 - Fix bug with reads split between R1 and R2 and identical names. Fix bug in log report (count per genus were wrong). Also add a few nice UI things (option --version, etc).

Add user option to use split paired-end (R1 and R2 files), and to modify the minimum read length after trimming. Also fix a typo in the readme

Improve Readme, add a dependency we were missing in the yaml, and fix a minor bug in extract_spacer that was created a useless extra output file

Fix minor bug with NA not carrying over when generating a new repeat table, and add some more checks and documentation for user input files

Transform into proper CLI

See merge request SRoux/spacerextractor!1

Adjust steps to build new db with custom MAGs/genomes/contigs, improve translate file to link the new CRISPR repeats to their db id

Update readme, some draft version of the scripts that would add user genomes to the db, starting with cctyper