Plotter: improvements and options for handling min and/or max lengths in len_dist plots

[AlexTate]

Improvements and options have been added for managing len_dist plot bounds. On the command line the min and/or max (first/last) lengths can be optionally specified with:

• --len-dist-min
• --len-dist-max

If either is unspecified, the unspecified bound is determined from the data's bounds on a per-subtype basis (i.e. the "Mapped" subtype bounds are determined separately from the "Assigned" subtype). Bounds, whether calculated or specified, are fixed across all plots for each subtype.

Run Config entries have been added for user specification:

• plot_len_dist_min
• plot_len_dist_max

If either of these values are unassigned, the workflow will first fall back to the corresponding entries for fastp (length_required and length_limit). These fastp values are also optional, so if they too are unspecified, then the workflow will not pass corresponding values on the command line and Plotter will default to determining bounds as described above.

Additionally:

• Plotter now ensures that the range of lengths plotted is continuous (no gaps) over a closed interval from min to max
• If min > max for one of the subtypes (e.g. if one of the bounds is unspecified and therefore calculated as such, or if a user mixes up the options) then Plotter will skip that subtype and print an error.
• The xtick label size is dynamically calculated in order to avoid crowding on the xaxis while maximizing size. If the calculated size is greater than the default size (xtick.labelsize in the stylesheet), then the default is used. If the calculated size is less than the min_size (which I chose to be 5 points), then the min_size will be used and a warning will be printed (this should be rare as it requires an exceptionally wide min/max delta)

The following demonstrates the new xtick label crowding mitigation (NOTE: see lower comments on this PR; the first plot is inaccurate):

Closes #191

[AlexTate]

Marking this PR as a draft.

As can be seen in the current plot for lengths 20-30, there is more work that needs to be done in properly subsetting the range while maintaining the original proportions. There is also room for improvement in the implementation of the new xtick label crowding mitigation

[AlexTate]

The above concerns have been addressed. PR is ready to be merged. Below is the corrected plot for lengths 20-30 which now shows correct proportions: