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andersen-lab / ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
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ivar trim -f option incompatible with new piping functionality #157

Closed wm75 closed 1 year ago

wm75 commented 1 year ago

With v1.4 ivar trim can write SAM to stdout, but when the -f option is in use the amplicon interval tree will still print itself to stdout, too https://github.com/andersen-lab/ivar/blob/98c2394639141a21c276f6c2e840c65fa1f6960c/src/interval_tree.cpp#L76-L82 , making those two functionalities incompatible for the moment.

cmaceves commented 1 year ago

thanks for brining this to my attention, we'll try and get it sorted out before it launches on bioconda!

wm75 commented 1 year ago

Well, that happened already, so it'll require a new release.

cmaceves commented 1 year ago

Yeah I just realized that... It'll have to be on our next version bump.