Consolidate/unify usage of chromosome coordinates

[suhas-r]

In various places in the code, we use chromosome coordinates in the form [chr1, pos1, o1]. This has a couple drawbacks:

• List usage. Despite having a fixed number of arguments, list usage means we're unable to enforce static type-checking on each argument as a result. Prefer shifting to namedtuples
• We have different "edge" definitions that concatenate these coordinates across multiple intervals, which makes indexing into these edges confusing.
  • ex: adding a discordant edge here in the form [chr1, pos1, o1, chr2, pos2, o2, sr_count, sr_flag, sr_cn, lr_count, reads, cn]. No typing, 12 indices to remember the unique meanings of. Modularizing the coordinates would help greatly, ex:

   class ChromosomeCoordinates(NamedTuple):
     chrom_num: int
     position: int
     orientation:  Literal["+", "-"]
  
   class DiscordantEdge(NamedTuple):
     start_location: ChromosomeCoordinates
     end_location: ChromosomeCoordinates
     ....