Dorado Alignments

[Adoni5]

Add some extension to the dorado plugin, causing it to set the alignments returned from dorado onto the basecalling result.

Not bothering with Guppy, as it's old.

Also sets reconnect_timeout and server_file_load_timeout to 10 on the PyBasecallClient by default meaning we timeout after 10 seconds rather than waiting for 5 minutes 5 times.

Add some code to the _mappy to create a PAF record from a list of fields, which is useful for converting the alignment data off the basecall record to a PAF.

Adds some documentation about using it to TOML.md.

Added the get_item function to deal with structured numpy arrays, which nested_get couldn't do ( I think ).

Notable

This method means it is absolutely possible to use both dorado to align as well as mappy, if mapper_settings isn't set to no_op.
Any thoughts?

[github-actions]

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