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… test status 10 in for non-path variants
shilpigoeldev
requested changes
Nov 19, 2025
lib/import/colorectal/providers/royal_marsden/royal_marsden_handler_colorectal.rb
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shilpigoeldev
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Nov 20, 2025
lib/import/colorectal/providers/royal_marsden/royal_marsden_handler_colorectal.rb
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shilpigoeldev
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Nov 21, 2025
NImeson
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What?
Adding in functionality to use the test status 10 value when recording the status of variant results. https://nhsd-jira.digital.nhs.uk/browse/NIT-357
Why?
The importer for Royal Marsden is not currently the test status 10 value to record abnormal, non pathogenic variants so requires updating
How?
Adding teststatus 10 in for non-pathogenic variants, as in the equivalent BRCA importer . Also added method to give those non-pathogenic variants (without a defined pathclass) a varpath class of 6 (where we know it is not pathogenic but don't know if it's class 1 or 2.
Updated tests to reflect changes made
Testing?
Variant counts match between current develop branch and this feature branch, all counts are the same. There aren't actually any test status 10 samples in the existing data.