This update is mainly an incorporation of NanopolishComp Eventalign_collapse into Nanocompore.
The output is compatible with the original format, but contains extra info and I also fixed an error in the number of kmers counted.
The documentation was also updated to account for the modifications.
While I was at it I also included a few other updates and fixes in other modules of Nanocompore:
Add a generic file parser which could maybe be used in SampComp later
Make Whitelist deterministic (hardcoded)
update and simplify the logging initialisation methods
Combine common CLI options together
Reworked multiprocessing framework for SampComp (Not tested with large datasets)
This update is mainly an incorporation of NanopolishComp Eventalign_collapse into Nanocompore. The output is compatible with the original format, but contains extra info and I also fixed an error in the number of kmers counted. The documentation was also updated to account for the modifications.
While I was at it I also included a few other updates and fixes in other modules of Nanocompore: