Closed scharch closed 5 years ago
Still using commit 00421b4158455e924d0a610ca0015c22465f4681
, btw
oh, it's because the --extra-annotation-columns
is supposed to be specified as a colon-separated list, like
--extra-annotation-columns invalid:in_frames:stops:cdr3_seqs:v_gl_seq:v_qr_seqs
I think like that ^ it only takes the last one that's specified. I think there is an argparse option that does behave the way you're expecting, but I'm not sure what it is.
At least this seems to fix it when I run that ^ command here.
I could swear it worked the other way before, but maybe I'm just loosing my mind. Will test next week and let you know.
I must be doing something really stupid here, because I know this was working a couple of months ago and I can't think of anything I've changed since then. Anything you can think of?
Note that cdr3_seqs and v_gl_seq are not columns in the output. They are not being output if I use yaml, either.