slow performance of ivar 1.3.2

[pdp10]

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]

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