Made mappability functions always ask for a genome seq file.

Previously there was an option to provide None, which was supposed to
use DEFAULT_ALL_GENOME_FILE which seems to have been removed from the
file earlier!  And anyway defaults are dangerous, so I modified the
functions to always require an explicit filename.

Unit-tests pass.  Also used it on real data, works.
Changed to file that actually exists (should be same data).
Minor: fixed error for no-colormaps case.
Better dealing with multiple splice variants in CDS start/end function.

Added NoRNAError and MultipleRNAError custom exceptions.

Changed get_gene_start_end_excluding_UTRs to raise these custom
exceptions in the relevant cases, rather than returning None.

Changed gene_positions to catch exception if desired, or else re-raise
it (previously it ignored the None if desired, else raised an
exception).

Unit-tests and run-tests still pass, but I don't think they're very
complete...
Adjusted to multiple splice variants, + general refactoring/docstrings.

Renamed _next_gene to _next_gene_for_mapp and expanded docstring to make
it clear what's actually going on!  Also renamed curr_pos to
curr_mapp_pos for the same reason.

Added dealing with multiple-splice-variant genes to _next_gene_for_mapp,
which is somewhat complicated - we want to count them for total gene
length, but not for binned gene length if it's supposed to exclude UTRs,
and not for feature mappable length... See comments/docstring for
implementation.

In gene_mappability:
 - added dealing with the MULTIPLE_SPLICE_VARIANTS feature in
   feature_total_mappable_lengths
 - added/removed some TODO/etc comments

Updated unit-tests (ONLY to add a MULTIPLE_SPLICE_VARIANTS:0 to the
results); they pass.
Changed feature_total_lengths to work with multiple splice variants.
Adjusted mappability_feature_barchart for multiple splice variants.
Minor: removed hardcoded gene total from genes_with_N_mutants.

Also changed plotting style a bit.
Adjusted _adjust_feature_mutant_counts for new feature types.

(Actually mostly using it to IGNORE new feature types.)
Also added MULTIPLE_SPLICE_VARIANTS to insertion_density_by_feature.

Tested insertion_density_by_feature on real data, works.
More options for dealing with UTR introns.

Previously I just added an option to _adjust_feature_mutant_counts to
treat UTR introns like UTR, which (probably) makes more sense
biologically, BUT it isn't how they're annotated in the simple datasets!
They're just annotated as introns, and it takes extra parsing to figure
out if they're normal or UTR ones.

So when I'm comparing to something like feature mappable length based on
a simple parsing of features, I need to treat UTR introns like introns.
Added an option for that; changed insertion_density_by_feature and
insertion_density_by_feature_pvalues to use that option. Also added a
separate long_UTR_names=False options rather than merging it into the
same thing. Updated docstring.
Minor: noticed minor issue with chromosome order, half fixed.
Implemented removing mutants from multiple files.

Simple implementation - just added a for loop. Updated help info.

Still needs a run-test!