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not all GFF3 feature types are displayed

See original GitHub issue

Created 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:

screen shot 2019-03-04 at 3 14 37 pm

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:closed
  • Created 5 years ago
  • Reactions:1
  • Comments:8 (6 by maintainers)

github_iconTop GitHub Comments

1reaction
jrobinsocommented, Mar 19, 2019

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.

0reactions
jrobinsocommented, Mar 20, 2019

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:

Hi @jrobinso https://github.com/jrobinso , as you’ve correctly pointed out, my gff3 file was not strictly gff3 valid. However, removing those problematic regions does not fix the underlying problem.

I’ll attach full-fat cleaned file (with mandatory .txt as @odoublewen https://github.com/odoublewen ) CP006569.1.gff.txt https://github.com/igvteam/igv.js/files/2987526/CP006569.1.gff.txt

In my case I thing that processing the gene and CDS category together (if they at same coordinates) would be excellent. However, other features like tRNA - etc are filtered out - which is not so great at all.

From what I could access (And I might easily be wrong) the gffHelper.js returns only the combinedFeatures and these are only the ones mentioned in my earlier post.

I you don’t want to change the behaviour significantly it still would be great to have some track option to set features to be displayed, potentially assign grouping options.

I can imagine something like

showFeatures = [ “tRNA”, “rRNA”, [“gene”, “CDS”], … ]

Best regards

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/870#issuecomment-474766534, or mute the thread https://github.com/notifications/unsubscribe-auth/AA49HMikekVgYsKfPF3-kjltYar1Rs6_ks5vYgkZgaJpZM4bdaDP .

Read more comments on GitHub >

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