Query length limit

[graceblackwell]

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.

[bingmann]

Yes, this is possible by copying some of the query code.
Will do.

[graceblackwell]

Oh great! Thanks

[shenwei356]

Hi @bingmann , how about canceling length limit?

[bingmann]

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.

[shenwei356]

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.

[bingmann]

This limitation has been removed in 05588df

Please tell me if the new master version works for you.