Directed selection for mikado prepare

[lucventurini]

Currently, in Mikado prepare, we perform two checks that might end up discarding transcripts:

1- a redundancy check, which will throw away multiple copies of transcripts regardless of their origin
2- a requirements check, which will throw away transcripts if they fail some basic checks.

Both steps are good and necessary, however, they need to be tweaked as follows:

1- during the redundancy check, transcripts should be prioritised according to their source score (if present). If a transcript source has been marked as "reference", those transcripts should always be kept.
2- During the requirements check, transcripts that have been marked as "reference" should always be kept.

[lucventurini]

Additionally, we should also make configure scoop up the status of a given assembly when loading from a sample sheet. Currently the functionality is implemented but not tested.

[lucventurini]

"Reference" transcripts will be treated as follows during the prepare step:

• A transcript which is marked as “reference” will never have its CDS stripped
• A transcript which is marked as “reference” will never be marked for removal due to redundancy, even if there are multiple copies of it, or if other assemblies with a higher score have identical transcripts (normally only one transcript would be retained, and that would be chosen amongst the highest scoring assemblies)
• A transcript which is marked as reference will never have its strand removed or flipped.

[lucventurini]

This issue is now putatively solved, although tests for it need to be implemented properly.
Shifting it to #137