Save BEAST2 posterior trees as readable by tracerer

[richelbilderbeek]

Currently, the BEAST2 posterior is saved in a way that is incompatible with tracerer.
To use the functionality of tracerer, this is desired.

I've labeled two tests with:

# TODO: Issue 100, #100

Sneak preview of one of these:

test_that("use", {

  # Create input files
  parameters_filename <- raz_create_tempfile("parameters.csv") # nolint internal function
  mbd_alignment_filename <- raz_create_tempfile("mbd.fasta") # nolint internal function

  # Run
  mbd_posterior_filenames <- raz_create_mbd_posterior_files( # nolint internal function
    parameters_filename = parameters_filename
  )

  # Check
  # All files exist
  expect_true(all(file.exists(mbd_posterior_filenames)))

  # MBD treees
  mbd_trees_filename <- grep(
    pattern = "mbd\\.trees$",
    mbd_posterior_filenames, perl = TRUE, value = TRUE
  )
  expect_true(length(mbd_trees_filename) > 0)

  # TODO: Issue 100, #100
  # tracerer must be able to read the posterior trees
  if (1 == 2) {
    # Current error: Error in value[[3L]](cond) : invalid file
    expect_silent(
      tracerer::parse_beast_trees(mbd_trees_filename)
    )
  }
  # ...
}