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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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slow performance of ivar 1.3.2 #154

Closed pdp10 closed 1 year ago

pdp10 commented 1 year ago

Is your feature request related to a problem? Please describe. In our pipeline, ivar was pinned to 1.3 (conda) and therefore we started using 1.3.2 as soon as this has been released. We noticed a significant slow down in performance (about 20 times slower). Pinning the version to 1.3.1 fixed our issue.

Describe the solution you'd like 1.3.2 should not be as slow as it seems to be

Describe alternatives you've considered We haven't had time to inspect the source code, but wondered whether there are specific reasons why the code has slowed us so much.

Additional context This is how we executed ivar: ivar trim -e -i 3e5abbe9-34cc-4425-b17c-46aac223aa0a.mapped.bam -b SARS-CoV-2.scheme.bed -m 30 -q 20 -p ivar.out It will take us some time to get the full log.

cmaceves commented 1 year ago

hi! we actually are aware of this issue. sorry for any inconvenience, and we're looking to push a quick bump next week to fix this, and the issue has been documented in issue #147