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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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Change in abpoa_msa function signature #38

Closed adcosta17 closed 2 years ago

adcosta17 commented 2 years ago

Hi,

I have abPOA integrated within another tool and I'm using it for consensus calling. I've been using the abpoa_msa function as previously described in the example.c file. With the latest version of abPOA I noticed that the signature for this function has changed, mainly it no longer allows for a consensus to be saved to a string in memory, but now expects only a C FILE pointer to write the output to file or stdout.

Is it possible to bring back or add an option to save the concensus in memory with the latest version?

Thanks

glennhickey commented 2 years ago

I ran into this too... it moved into abpoa_cons_t which gets made by apoa_msa via the abpoa_t input. You can leave the FILE pointer NULL.

yangao07 commented 2 years ago

@glennhickey is right, abpoa_cons_t includes a set of variables related to consensus calling result. For FILE pointer, leave it as NULL if you want to store consensus in variables, example.c shows how to use it.

adcosta17 commented 2 years ago

I made the changes and its working well. Thanks!