not all GFF3 feature types are displayed
See original GitHub issueCreated a simple GFF3 (believe it is valid) with 4 feature types:
##gff-version 3
chr1 internal exon 1000 1100 . + 1 ID=feature_with_type_exon
chr1 internal CDS 1100 1200 . + 1 ID=feature_with_type_CDS
chr1 internal contig 1200 1300 . + 1 ID=feature_with_type_contig
chr1 internal gene 1300 1400 . + 1 ID=feature_with_type_gene
Only 2 of the 4 types display in igv.js:
My test files for this issue are in this diff (comparing my fork of this project): https://github.com/igvteam/igv.js/compare/master...odoublewen:master
Issue Analytics
- State:
- Created 5 years ago
- Reactions:1
- Comments:8 (6 by maintainers)
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Everything is tuned for the latter, in 10 years this is the first time this issue has arose. Plenty of issues have arising around transcripts, there is too much freedom in gff and many ways to model. Also unusual things like exons with multiple transcript parents. That’s how the code got so complicated. I’m considering a new approach that would work for both, but again this is the first time the issue has arose in 10 years so its hard to prioritize. A less complex code base might be motivation enough, I will take a fresh look at it.
OK, thanks. Filtering tRNA out is definitely a bug. I can imagine certain features, like stop codons without parents, being filtered but not many. I will look into this.
On Wed, Mar 20, 2019 at 3:10 AM SchwarzMarek notifications@github.com wrote: