GitLab

Hotfix/primary assemblies

Add missing set_hstart_hend function

I'm not sure this modification is really needed. It definitely works
and it makes the code cleaner

Some species don't have contigs so it's better to use seqlevel
as it will return either contig or primary_assembly depending
on the database

Species without contigs need the INSDC synonym to be present to return
the correct data for the XML file
Use INSDC instead of insdc as sqlite is case sensitive

If we use the locus cache to fetch the new locus before it was
added to the cache we will modify the old one and ZMap will
not be able to delete the correct object in the display

Changed authentication process to use prod authentication server

Do not check pipeline table if primary_assembly

Module to fetch data from a compara database

Added herring and herring test species

Temporary changes to the authentication process. Merging it as it does not affect anything serious.

Added mouse test species details

Store evidences fix

Add supporting evidences when cloning object

Display CS name instead of Assembly in clone window

The new_dissociated_copy method in Exon and Transcript was not copying
the supporting evidence. So the supporting evidences would be lost each
time the method is used

Changes made for fetchdb to work in ZMap

Revert "Revert "Store evidences""

We are excluding list of old transcript types from dropdown

Fix coordinate system name while we are finding chromosomes

Debug output for search