search

tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections
GNU Affero General Public License v3.0
77 stars 7 forks source link

Possibility to output raw counts ? #9

Closed hl-xue closed 3 years ago

hl-xue commented 3 years ago

Hello,

Thanks for developping this nice tool ! I found the output counts are scaled into 0-255 by default, and I was wondering if there is some way to have the raw counts as output without scaling ?

Thanks and best wishes.

tlemane commented 3 years ago

Hello,

Thanks for trying kmtricks! Yes by default the maximum is 255 to use only one byte per count. You can change this value using --max-count N.

hl-xue commented 3 years ago

Thanks for reply. So the N is a value ? So in case I don't know the maximum of the count and I would like to put a very big N, is there any limit of this value (e.g. 32-bit integer)?

tlemane commented 3 years ago

Yes kmtricks can use 8, 16 or 32-bit unsigned integer to store counts. So the maximum is 232-1.

hl-xue commented 3 years ago

OK, thanks a lot ! Best wishes.