Skip to content

Fixed bug when core dbs don't have contigs

Marek Szuba requested to merge github/fork/JAlvarezJarreta/master into master

Created by: JAlvarezJarreta


Removed assumption that the 3 levels of assembly are chromosome, supercontig and contig, as there are many other species with different coord_system sequence level (e.g. primary assembly, scaffold).

Furthermore, a similar error might be raised in the future regarding supercontigs, and since toplevel and seqlevel are linked in the assembly table, that part of the code has also been removed.

Possible Drawbacks

If the intermediate coord_systems are required to be cloned, a new piece of code that loops over the ranks between toplevel and seqlevel should be implemented.


The code has been tested within a new pipeline to create a new Compara master database from scratch and the given regions of each species have been cloned correctly, regardless if they have contigs, primary assemblies (clown fish) or scaffolds (wheat) as seqlevel.

Merge request reports