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jermp / lphash

Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
MIT License
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Multithreading for query-p command #19

Closed tbenavi1 closed 1 year ago

tbenavi1 commented 1 year ago

Hello,

Would it be possible to implement multiple threads for the query-p command. In particular, a very simple implementation would just be to have each thread analyze a different subset of the sequences in the input fasta file. Thanks for any assistance.

jermp commented 1 year ago

Hi, yes, we could use the excellent parsing library by Rob Patro, https://github.com/rob-p/FQFeeder. See an example here https://github.com/jermp/fulgor/blob/main/tools/pseudoalign.cpp on how to use it. I will probably add this to LPHash query command as well, as soon as possible!

Thanks and best, -Giulio

tbenavi1 commented 1 year ago

Thank you.