Version 1.18 of tabix exhibits poorer performance in querying locus information compared to version 1.16. about htslib HOT 2 CLOSED

I've tried and cannot reproduce this. Infact 1.18 is faster than 1.16. Were all your binaries built with the same compiler and compiler version, with the same options?

Also, are you using -T or -R for queries? Have you tested speeds on both? At some point -T becomes faster than -R (where the density of hits becomes sufficient). This feels wrong, and it ought to asymptotically approach instead of passing. It implies the index jumping option (-R) is unnecessarily decoding things multiple times. We fixed this in the multi-region iterator for SAM and BAM, but I guess tabix has its own iterators. That's a different issue though and not related to 1.16 vs 1.18.

from htslib.

Alright, I'll go and confirm the versions and parameters of the compilation tools for versions 1.16 and 1.18. Anyway, thx!

from htslib.