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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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Issue 147 #151

Closed cmaceves closed 1 year ago

cmaceves commented 1 year ago

meant to address issue #147 for milestone 1.3.3. currently insertionSort is called many times, leading to a large slowdown in ivar trim. this fix changes the codebase to only call insertionSort one time and updates tests to reflect placement of call outside of get_overlapping_primers.

cmaceves commented 1 year ago

time fold improvement > 10x

gkarthik commented 1 year ago

Merged into trim_io which will subsequently be merged into master.