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Remove excess calls to insertionSort #147

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cmaceves opened this issue Feb 7, 2023 · 3 comments
Closed

Remove excess calls to insertionSort #147

cmaceves opened this issue Feb 7, 2023 · 3 comments
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@cmaceves
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cmaceves commented Feb 7, 2023

In the code for primer trimming insertionSort gets called every time get_overlapping_primers is called, creating a slowdown

std::vector<primer> test = insertionSort(primers, primers.size());

This should only be called once.

@cmaceves cmaceves added the bug Something isn't working label Feb 7, 2023
@cmaceves cmaceves added this to the v1.3.3 milestone Feb 7, 2023
@cmaceves cmaceves self-assigned this Feb 7, 2023
@tseemann
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@cmaceves we switched to ivar 1.3.2 last week and noticed it was taking 10x (!) longer to run on our 384 samples (~1 M reads each).

Would this bug explain the slowdown in ivar trim?

@cmaceves
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hi @tseemann! that's correct, it is causing the slowdown. we're aiming for a fast turn around time on 1.3.3 to address that oversight.

@cmaceves
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addressed in PR #155

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