These are chat archives for dereneaton/ipyrad

17th
Jan 2016
Isaac Overcast
@isaacovercast
Jan 17 2016 03:20
In params.txt for params with multiple values (e.g. edit_cutsites or restriction_overhang) i think we should make it so everything is entered comma separated, no perens or brackets. That way we can split on ','. Trying to make reading params.txt and write_params() agree on behavior, seems simplest is best.
Deren Eaton
@dereneaton
Jan 17 2016 05:39
Yeah, that sounds right to me.
Isaac Overcast
@isaacovercast
Jan 17 2016 20:49
In cluster_within.clustall() what would be the case where concat_edits would be needed? When would a sample have multiple edits files? I'm cleaning up step3, refmap isn't doing a call to concat_edits, so if this ever were the case it will be wonky.
Deren Eaton
@dereneaton
Jan 17 2016 23:32
I think I had envisioned making a link_edits function so users could read in prefiltered data and skip step 2, but not that I think about it seems unnecessary. They should just do link_fastqs and run step2.
Deren Eaton
@dereneaton
Jan 17 2016 23:39
I'm working on getting all the filters working in consen. And I just got my hands on some empirical pairddrad.