[Seqan-dev] FaiIndex + getIdByName/readRegion not threads-safe

[Johannes Dröge <johdro@mpi-inf.mpg.de>]

Hi Seqan team,

I recently ported my code to use an off-memory sequence store with your FaiIndex class. Here is the problem: Whenever I use more than two threads to read a region using getIdByName+readRegion, the region returned is incorrect. The class does not seem to be thread-safe, although I cannot image why read-only functions like the above should not be run in parallel. I could wrap the lookup into a class with a locking mechanism but I imagine it would be easy and quick to fix the class without introducing unnecessary locks.

When I give readRegion an object of type "const FaiIndex", it segfaults. IMO, whenever your index is read-only, the methods should be thread-safe or not available at all.

Gruß Johannes