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yangao07 / abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
MIT License
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-S option for pyabpoa #47

Open christopher-vollmers opened 1 year ago

christopher-vollmers commented 1 year ago

Hi,

My lab's Mandalorion and C3POa tools use pyabpoa and it works great. Just every once in a while, we encounter an overlong sequence and pyabpoa stalls for a very long time.

I've noticed that abpoa has the -S option to do seeded alignment, potentially using a lot less memory in the process. Is that option available for pyabpoa as well? I can't seem to find that info.

Thank you, Chris

yangao07 commented 1 year ago

Hi Chris,

You are right, the python version of abPOA does not have the seeding option right now. It is possible to add this feature.

I will get back to you later.

Yan

yangao07 commented 1 year ago

Also, you may want to try the abPOA program with -S enabled on your data first, to see if you can get the expected result.