Is it possible to re-use wfagpu_aligner_t for multiple alignments?

[fkallen]

From the code examples and API, it seems the following is the standard use case.

for each batch{
      wfagpu_initialize_aligner
      wfagpu_add_sequences from batch
      do settings
      wfagpu_align
      wfagpu_destroy_aligner
}

Is it possible to initialize the aligner once, and re-use it for all batches? This would avoid memory allocation for each batch.

wfagpu_initialize_aligner
for each batch{
      ???  reset aligner without reallocation ???

      wfagpu_add_sequences from batch
      do settings
      wfagpu_align
      
}
wfagpu_destroy_aligner

[quim0]

Hello,

Right now, it's not possible, the batching is handled by WFA-GPU itself (probably not the best design decision...), you need to add all the sequences and then adjust the batch size using wfagpu_set_batch_size (see this example). Let me know if that works for you.