Option to filter gap-only columns from output alignment

[darcyj]

Hey Elmar,

It would be really useful if SINA could simplify its output alignment a bit, by removing columns that contain only gap characters. Currently I'm using the QIIME1 script "filter_alignment.py" to do this.

Thanks!

-JLD

[epruesse]

Also: allow adding gaps to reference alignment

@darcyj What would you expect the option to be called? --fasta-compress-gaps, --compress-gaps, --remove-gap-only-columns, ...? And the one for adding gaps?

Thinking to only allow "multiplying" the alignment width (add n gaps between columns and surrounding alignment).

[darcyj]

Maybe it would be nice to mirror the old option in ARB's exporter, like --compress-vertical-gaps, although I think the word "compress" is somewhat misleading. I like --remove-vertical-gaps or --remove-gap-only-columns which is very explicit.

For adding n gaps between each column, maybe something as simple as --add-vertical-gaps or --add-gap-only-columns because it would compliment the above option. I agree with you, that sounds like an interesting feature, so that one could make a reference alignment for a clade of interest, and have room within that alignment for insertions.