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soedinglab / hh-suite

Remote protein homology detection suite.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
GNU General Public License v3.0
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Fix buffer overflow in ffindex_from_fasta #265

Open konstin opened 3 years ago

konstin commented 3 years ago

I could verify with valgrind that previously that this could lead to memory corruption.

Is there any suggested way to check if that has an impact on performance?

ahcm commented 2 years ago

Mainline does not have this problem: https://github.com/ahcm/ffindex

konstin commented 2 years ago

@ahcm What's the relation between this repository and https://github.com/ahcm/ffindex? I was under the impression that ffindex is a part of and maintained by the hh-suite

ahcm commented 2 years ago

I wrote FFindex as the database format for Johannes' hhblits, when we were colleagues at LMU. So it's quite OK to package it. Unfortunately the code changes they made range from unnecessary to dangerous, introducing strange limitations and security flaws.

The switch to cmake I can understand, but think it's not worth the trouble.

To be honest, I never understood why they forked it when they left Munich. Debian/Ubuntu uses mainline and also their hhsuite package depends on it.

So I assume all features are present in mainline. If not just file an incident on mainline GitHub.