Refactor binsplitting

[jakobnissen]

There are multiple problems with the way we do binsplitting now, which I would like to address is this larger PR:

• We either output split bins or unsplit bins, where it would be more useful to output both, if possible (Output source clusters for bins when binsplitting #237).
  • In this PR, both files are always written if binsplitting takes place.
• We default to no binsplitting, even though we know this produces worse output. Ideally, we'd like for Vamb's defaults to be optimal.
  • In this PR, we default to binsplitting with 'C'.
• If users pass in a wrong binsplit separator, e.g. by mindlessly copy-pasting -o C into the command without realising what it implies about the naming scheme of the identifiers, then Vamb errors only at the clustering step after training. Ideally, this would error already when reading in the FASTA file.
  • In this PR, it errors when parsing the FASTA file if the separator is not found, UNLESS the user did not specify any separator and it just defaulted to 'C'. In this case, it will warn the user, and then disable binsplitting
  • The error message is improved in this PR
• The logic of binsplitting is too complicated, because binsplitting takes place at multiple different levels: Immediately after instantiating the clusterer, when writing the cluster file, or when writing the bins file.
  • In this PR, only binsplit immediately before writing to files.
  • Also, in this PR, the printing functions should not binsplit. Instead, binsplit the clusters, then print them

Further,

• I have removed the -i option. This is not generally useful. We should instead output total bin size and other bin statistics to users and let them decide (Meta-issue for improving user-friendliness #240)

To do

• Refactor the clustering and writing of clusters in __main__.py to deduplicate code
• Address TODOs
• Make sure the program runs normally
• ....and respects -o X and -o
• ...and respects -c X
• Make tests pass

Closes #237

[jakobnissen]

CC @sgalkina - can I have your review on this (if you have time?)

This is a larger PR. I tried to break it into commits but it didn't work out. These are the conceptual large-scale points of change which you can review:

• Removed the -i option. I think we don't really need this as a CLI parameter. I also had some real reason for removing it, but I can't really remember now.
• In parsecontigs.py, move the warnings to __main__.py, since it's really a user-facing warning meant for CLI use
• In vambtools.py, Added a BinSplitter class responsible for binsplitting. This is useful now because the binsplitting logic is somewhat more complex to make it more user friendly.
• In vambtools.py, simplify write_clusters and write_bins, such that they have no binsplitting or filtering obligations. Instead, binsplitting and/or filtering must be done before passing to these functions.
• Refactoring __main__.py. Mostly just adapt the above changes, but also add cluster_and_write_files and write_clusters_and_bins to cut down on code duplication

[jakobnissen]

OK, gonna merge this