Show modified bases using MM and MP/ML tags in BAM/CRAM

[cmdcolin]

Stub for coloring reads that have MM (positions of modified bases) and MP/ML (modification likelihood/probability) tags

This can be used to show methylation and other types of modifications, but methylation is probably the most common application

https://github.com/GMOD/jbrowse/issues/1588

Needs to still incorporate CIGAR for positioning, but this is a fun start

Requested here https://github.com/GMOD/jbrowse/issues/1588

[cmdcolin]

Note that to do this properly, it is probably useful for SNPCoverage to also show these modification in the pileup too

[cmdcolin]

Other todos:

• incorporate into snpcoverage renderer/adapter
• dynamically set color palette for different modifications (similar to our color by tag functionality)
• allow only drawing a single modification type at a time perhaps
• possibly draw multiple modifications at a single base pair

[cmdcolin]

possibly also making the wgbs type display could be worth doing in parallel, as some modern tools for calling modifications output pseudo-wgbs mode bam files https://software.broadinstitute.org/software/igv/interpreting_bisulfite_mode

[rbuels]

looks good, just a couple little questions

[garrettjstevens]