Parallelizing certain operations

[fedarko]

Will take some extra work, but may be worth it for some really long-running stuff.

Things that are embarrassingly parallelizable across contigs

• align

  • OSA filter (just pass 2, I think?)
  • Maaaybe the PM read filter

• call

  • The main loop through contigs can be done independently

• fdr estimate

  • Computing target contig FDR curve info

• spot cold-gaps

  • Each contig can be processed independently

• smooth

  • apply: Each contig's smoothed and virtual reads can be created independently
  • assemble: Each contig's reads can be assembled independently