implement progress bar for pileup

[jayhesselberth]

closes #49

Rough implementation of a progress bar for run_cpileup.

Ideally the progress would be based on the number of sites to be evaluated instead of NA_REAL and n_iter, but I'm not sure where that information is stored.

Currently it counts up; if based on the number of sites I think this would convert to a percentage based countdown:

Based on https://cli.r-lib.org/articles/progress-advanced.html#the-c-api

[jayhesselberth]

I also increment n_iter in this PR; it didn't look like it was being used (and so the interrupt check was useless).

[jayhesselberth]

This is does something really strange when using BPPARAM; the spawned processes don't really consume CPU, and may spend all their time updating the progress bar?

[kriemo]

BiocParallel doesn't pass messages from the workers during execution, only at the end, or in log files, so that might be causing the issue?

Once the c code has been more finalized I'll test out and incorporate cli if possible, as this would be a very nice feature. In the meantime you can report progress using biocparallel, which will update the progress bar at each iteration, which for get_pileup() will be at each chromosome.

e.g. (p

library(BiocParallel)
bpp <- MulticoreParam(workers = 3, progress = TRUE)
bplapply(seq(1, 10, by = 2), Sys.sleep, BPPARAM = bpp)

[jayhesselberth]

Closing for now, the built-in BiocParallel progress bars seems good enough for most use cases:

bpp <- MulticoreParam(
  workers = 24,
  progressbar = TRUE
)

pileup_sites(..., BPPARAM = bpp)