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  1. Jalview
  2. JAL-3121

Allow export/import of map-value feature attributes via GFF3

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 2.11.0
    • Fix Version/s: 2.11.1, 2.11.1.0
    • Component/s: None

      Description

      Map-value feature attributes were introduced to support import and persistence of attributes from VCF files (e.g. CSQ:clinical_significance). In Jalview 2.11, these attributes are not exported in GFF3 and there seems to be no way of creating them from an imported GFF3 file.

      Note: hierarchical maps are not that common in GFF3 files so we may need to come up with our own formalism for how VCF map-values can be safely round-tripped to GFF3.

        Attachments

        1. NMT1_CDS.fa
          4 kB
        2. NMT1_CDS_features.txt
          2.02 MB
        3. estrogenReceptorCdna.gff
          0.2 kB

          Issue Links

          is duplicated by

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3419 Roundtrip of feature 'otherDetails' via gff format

          • Major - Major loss of function.
          • Closed
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-3304 Export linked features

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2927 Export Feature Description in GFF

          • Critical - Crashes, loss of data, severe memory leak.
          • In Progress

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: