get_combined_quant_gtf - retain matching reference transcript ID from novel GTF

[SamBryce-Smith]

https://github.com/frattalab/PAPA/blob/aa034556b3bb96448eb58044b7414e34f2a42862/scripts/get_combined_quant_gtf.py#LL663C1-L663C1

Makes downstream analysis with last exons only an incredible pain in the behind...