Adding gff support for NearestExonJB plugin - #856
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August 13, 2026 08:25
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Summary
This PR allows NearestExonJB to retrieve exon locations from a tabix-indexed GFF3 file:
--plugin NearestExonJB,gff3=/path/to/genes.gff.gzIt also adds parent_only=1, which excludes exons from readthrough transcripts, artifact genes, and unsupported GFF gene-parent types.
To test...
Use this variant:
1 1243545 . G ACompare the database-backed plugin:
--plugin NearestExonJB,intronic=1with the GFF-backed plugin:
--plugin NearestExonJB,gff3=Homo_sapiens.GRCh38.116.chr.gff.gz,intronic=1,parent_only=1Using the release 116 GFF, both modes should annotate the same transcripts and exon boundaries:
ENST00000330388.2 ENSE00001299832+7+end+109
ENST00000468365.1 ENSE00001882488+7+end+287
ENST00001086007.1 ENSE00001299832+7+end+109
ENST00001145430.1 ENSE00001299832+7+end+109
ENST00001086006.1 ENSE00004705606+393+end+91 ENSE00001311835+409+start+152
The other transcripts should have nothing.