[fast-contrib]: issue: learnt index generation does not run minimap2 with avx512 define by default

[harisankarsadasivan]

Hello, ./build_rmi.sh test/MT-human.fa map-ont does not run mm2 with avx512 by default. I understood this from the print statements "Using default hash lookup" from main.c. Is there a reason why this is the case? @lh3 @SaurabhKalikar

[SaurabhKalikar]

Hi @harisankarsadasivan

The script build_rmi.sh builds machine-learning based learned index structure to accelerate seeding phase. For building the index, the script runs default (non-AVX512) minimap2 to collect all minimizers of a reference sequence, and then uses these collected minimizers to train the index structure. The trained index structure is stored into a file and is used when mm2-fast runs with lhash (learned hash tables) enabled. Building index is just one-time task. Besides we don't have AVX512 acceleration of minimizer collection stage. So it is either default hash lookup based approach or the one with learned-indexes.

Thanks, Saurabh