Optionally mask the start/end of sequences

[matthuska]

In GitLab by @hoelzer on Jun 21, 2021, 09:51

It would be great if CovSonar can mask start/end of a sequence (similar to what Nextstrain does, ...), e.g.

• --mask_start 200
• --mask_end 200

The ends are often fuzzy and can lead to false positively called substitutions/indels. If such sites are included in the profiles subsequent tasks such as clustering (breakfast, ...) might fail

EDIT here how Nextstrain does it:

https://github.com/nextstrain/ncov/blob/master/defaults/parameters.yaml

# Mask settings determine how the multiple sequence alignment is masked prior to phylogenetic inference.
mask:
  # Number of bases to mask from the beginning and end of the alignment. These regions of the genome
  # are difficult to sequence accurately.
  mask_from_beginning: 100
  mask_from_end: 50