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Use flush_Transcripts method to correctly empty the _transcript_array

Marek Szuba requested to merge github/fork/thibauthourlier/hotfix/transcript_save into feature/ensembl_friendly

Created by: thibauthourlier

Since release/85 get_all_Transcripts returns an arrayref on the copy of the array of transcripts array instead of the actual reference. So when the code was deleting the old_gene using later version of the code it was also deleting the transcripts. This was not intended.

This has been lightly tested

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