mphfKind is not stored in hdf5 file

GATB / gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

https://gatb.inria.fr/software/gatb-core/

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mphfKind is not stored in hdf5 file #15

Closed Piezoid closed 7 years ago

Piezoid commented 7 years ago

Hi.

Opening a graph generated with an emphf table (for example a graph generated with Minia) trigger a segfault.

The problem is that GraphTemplate (const std::string& uri) initialize _mphfKind to MPHF_BOOPHF, then the map is loaded with the BooPHF implementation, triggering the crash.

I tried to implement the detection but found that mphfKind is not stored in /configuration/xml nor in /mphf/xml. grep -i emphf confirmed that the string is not present.

rchikhi commented 7 years ago

Good catch. Temporary fix: set "-mphf boophf" when running the software. We're getting rid of _mphfKind and emphf in the next release, in favor of BooPHF enabled by default in Graph.