GitLab

make sure each transcript even if it is in a differernt gene have differernt transcript ext for the same gene name

used to process the mappings if species.pm file is not found.

Test case addition to make sure we don't keep on iterating executing the transaction when its been successful

Added code to fix issue with Corf genes in zebrafish. The gene names were not being modified to look like hsC*orf*-like. This now works.

Added an additional check in the transform method. When testing exons, if consecutive exons in the old version of the transcript were on the same strand then the new versions should be on the same strand too. If not, returns undef. Prevents cases being transformed where the transcript's exons map as below:

1
------------------------------
-1        5  4  3  2  1

to

1      3  4  5
------------------------------
-1               2  1