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  1. Jalview
  2. JAL-3375

Better VCF numeric data field validation while parsing (e.g. AF* attributes)

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.0
    • Fix Version/s: 2.11.1, 2.11.1.0
    • Component/s: variants
    • Labels:
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      Description

      AF* attributes are not detected as numeric due to malformed zeroes "0.00000e 00" (with embedded space) in the gnomAD exome data.
      As a side-effect, these fields are treated as character, not numeric, in the feature filter dialog.
      These invalid values (and also '.') should be ignored when parsing so only valid values are recorded (and numeric filtering enabled).

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            Assignee:
            gmungoc Mungo Carstairs
            Reporter:
            gmungoc Mungo Carstairs
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              Updated:
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