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#gffTags handling in .bed files in igv.js arguably ought to comport with that of IGV desktop #1550

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malcook opened this issue Oct 6, 2022 · 0 comments

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@malcook
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malcook commented Oct 6, 2022

In IGV desktop it is documented that "GFF3-style attributes (in) the Name field (column 4) of a BED file ... are displayed in the popup text. " and "The GFF Name property will become the display name of the feature" when using the #gffTags directive.

Consistent with the this, if there is no Name attribute, the display name of the feature is blank.

In my hands, in igv.js with or without a #gffTags, the popup text is taken from column 4.

This seems reasonable to me, except, there appears to be no control over the display name of the feature.

It would be good if IGV and igv.js agreed in their handling of gffTags, so that the same .bed files can be used to similar effect in both platforms.

I tried as a workaround loading the track with nameField: null and nameField: 'IGNORE' and nameField: 0 but none had the desired effect of suppressing a display name.

FWIW: I also find that the overall length of the GFF3 encoded attributes is limited in igv.js as compared to IGV desktop.

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