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  1. UGENE
  2. UGENE-4564

Opening of VCF file with invalid lines

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    Details

    • Story Points:
      5
    • Tests Type:
      Functional/Unit
    • Sprint:
      DEV-26/08/2015, DEV-22/09/2015
    • Affect Type:
      Userdefined

      Description

      Variants in a VCF file are stored in lines, i.e. each variant is described in one line. Therefore, if a line is invalid, it can be skipped and the file can be parsed further.

      In the current UGENE version, when a VCF file contains an invalid line, the file is not opened and an error notification is shown.

      The following should be done instead:

      • The valid records must be visualized in the GUI
      • A warning notification must appear. When the notification is clicked, a report is opened. The report contains detailed information about each invalid record: the line number and the problem occurred.

      Sample VCF files are attached:

      • G55421.annotated.vcf - the file can't be opened in UGENE, but can be in IGV.
      • G55414.annotated.vcf, G55430.annotated.vcf - the files can't be opened in neither in UGENE, nor in IGV.
      • G55431.annotated.vcf - can be opened without errors.

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            People

            Assignee:
            ggrekhov German Grekhov
            Reporter:
            oigl Olga Golosova
            Assigned Tester:
            Eugenia Pushkova [X] (Inactive)
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: