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trycycler reconcile: multiprocess get_pairwise_alignments #63

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danpal96 opened this issue Jul 24, 2023 · 2 comments
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trycycler reconcile: multiprocess get_pairwise_alignments #63

danpal96 opened this issue Jul 24, 2023 · 2 comments
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enhancement New feature or request

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@danpal96
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trycycler v0.5.4

One of the slower steps in trycycler reconcile is the call of the get_pairwise_alignments function

Trycycler/trycycler/pairwise.py

Line 20 in c00d56f

def get_pairwise_alignments(seqs):

I think the for loop could be parallelized and if you want I can make a PR.
Regards,
Daniel Palma
@rrwick rrwick added the enhancement New feature or request label Aug 1, 2023
@rrwick
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rrwick commented Aug 1, 2023

You're right - that step can be a bottleneck, especially for longer contigs.

You're welcome to put together a PR, if you'd like - thanks!

@danpal96 danpal96 mentioned this issue Aug 2, 2023
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@rrwick
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rrwick commented Aug 8, 2023

Thanks for the PR 😄

@rrwick rrwick closed this as completed Aug 8, 2023
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@rrwick @danpal96