Query length limit
graceblackwell opened this issue · 6 comments
Would it be possible to increase the query length limit? I am wanting to query sequences up to 300kb and it would be good to avoid having to split the sequences up into chunks.
Yes, this is possible by copying some of the query code.
Will do.
Oh great! Thanks
Hi @bingmann , how about canceling length limit?
What do you mean with cancel?
The score counters can be 16-bit (max 65 Ki query length), or 32-bit (max 3 million query length), 64-bit would also be possible, but expensive memory-wise.
I see, I just figure out that 65535 is the maximum 16bit uint, where you use _mm_add_epi16 for parallelizing k-mer count for 8 documents. So replacing _mm_add_epi16 with _mm_add_epi64 can break the limit, in cost of little more memory usage.