file_transformation:
  - Added prefixes to GFF references and IDs

changes:
  - 2018-03-01 moved file lists into MANIFESTs
  - 2018-06-25 added descriptions file: arahy.Tifrunner.gnm1.ann1.CCJH.info_descriptors.txt - derived from gff3 file as follows: cat arahy.Tifrunner.gnm1.ann1.CCJH.gene_models_main.gff3 | awk '$3=="gene"' | grep "Name=" | grep Z7AAAI | perl -pe 's/%2C/,/g; s/%3B/;/g; s/%3D/=/g'
  - 2019-05-20 Updated README to note publication
  - 2019-07-25 Updated GFF file to fix problem with parent names in exon records (second and subsequent names within an exon with multiple parents had incorect forms).
  - 2020-04-03 adf updated GFF file to fix lingering issues with shared exons and suppressed transcripts reported by user
  - 2020-04-27 use bgzip+samtools faidx for derived fastas
  - 2022-08-09 adf: fix bgzip and tabix for gene models main file
  - 2023-02-12 adf: fix non-unique IDs per https://github.com/legumeinfo/datastore-issues/issues/153 using datastore-specifications/scripts/add_IDs_to_gff_features.pl --clobber CDS --clobber five_prime_UTR --clobber three_prime_UTR
  - 2024-12-10 sc: Add back prefix Arahy. to Tifrunner gene IDs and Names
  - 2025-04-16 adf: add arahy.Tifrunner.gnm1.ann1.CCJH.legume.fam3.VLMQ.gfa.tsv.gz