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  1. Jalview
  2. JAL-3527

Offer program specific IO options for GFF files

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
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      Description

      Some programs have different levels of support for GFF, and custom interpretations

      IGV seems to allow pragmas for changing how the fields are interpreted (or shown) - e.g. https://software.broadinstitute.org/software/igv/GFF ##displayName can be used to specify the display name field. The Column 9 'Color' attribute can be used to specify the colour for a feature.

      UCSC Genome browser only supports GFF2 - and treats column 9 as a 'group' tag (putting all features with the same col. 9 value in the same group) - so an option to restrict or simplify the output of column 9 could be useful here. see https://genome.ucsc.edu/FAQ/FAQformat.html#format3


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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated: