error in gff file (rnaseq branch test-datasets/reference/genes.gff)

We found a problem in the gff file you have as test.

• rnaseq
• test-datasets/reference/genes.gff

I	ensembl	transcript	335	649	.	+	.	ID=YAL069W;Parent=YAL069W;geneID=YAL069W;gene_biotype=protein_coding;gene_name=YAL069W;gene_source=ensembl;gene_version=1;p_id=P3634;transcript_biotype=protein_coding;transcript_source=ensembl;transcript_version=1;tss_id=TSS1129
I	ensembl	exon	335	649	.	+	.	Parent=YAL069W;exon_id=YAL069W.1;exon_number=1;exon_version=1;gene_biotype=protein_coding;gene_name=YAL069W;gene_source=ensembl;gene_version=1;p_id=P3634;transcript_biotype=protein_coding;transcript_source=ensembl;transcript_version=1;tss_id=TSS1129
I	ensembl	CDS	335	649	.	+	0	Parent=YAL069W;exon_number=1;gene_biotype=protein_coding;gene_name=YAL069W;gene_source=ensembl;gene_version=1;p_id=P3634;protein_id=YAL069W;protein_version=1;transcript_biotype=protein_coding;transcript_source=ensembl;transcript_version=1;tss_id=TSS1129

ID and Parent attributes of transcript features have same IDs. This is not allowed in GFF3 specifications.

We use AGAT that deals with that problem by automatically updating the parent ID to be uniq.
Using this file to test/build pipelines might be problematic. This should be updated.

Inspect test-datasets/reference/genes.gff on the rnaseq branch and compare the transcript ID and Parent attributes with the GFF3 specification. Use AGAT to verify the corrected fixture no longer requires automatic parent-ID rewriting; done means the test file contains unique, valid identifiers.