DEVSU-3003 Do not display variant in TGR moves to VUS

[bnguyen-bcgsc]

• DEVSU-3003
• Fix bug where variants with noTable tag gets included in table of unknown significance variants instead
• Update unit test

[codecov-commenter]

Codecov Report

❌ Patch coverage is 77.77778% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.86%. Comparing base (1a3e0a2) to head (a6bac45).

Files with missing lines	Patch %	Lines
app/routes/report/variants.js	77.77%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #512      +/-   ##
===========================================
+ Coverage    76.83%   76.86%   +0.03%     
===========================================
  Files          190      190              
  Lines         7029     7034       +5     
  Branches       920      921       +1     
===========================================
+ Hits          5401     5407       +6     
+ Misses        1530     1529       -1     
  Partials        98       98              

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[Copilot]

Pull request overview

This PR addresses DEVSU-3003 by ensuring variants explicitly tagged noTable are not included in the Rapid Report “unknown significance” (table 3) output when they would otherwise be pulled in via gene-property qualification (especially when there are no KB matches). It also adds a regression test to cover the scenario.

Changes:

• Exclude noTable-tagged variants from the unknown-significance results even when gene properties qualify them.
• Track noTable-tagged variant idents to prevent re-adding them during gene-property backfill and to filter them out at return.
• Add a unit/integration test covering “no KB matches + gene qualifies + noTable tag” behavior.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
app/routes/report/variants.js	Adds noTable ident tracking to prevent gene-property-based inclusion into unknown significance, and filters out noTable results.
test/routes/report/variants.test.js	Adds a regression test ensuring a noTable-tagged variant with no KB matches does not appear in table 3.

Suppressed comments (2)

app/routes/report/variants.js:192

• Avoid using console.log in the API route; the rest of this module uses the shared Winston logger. Also, doNotReport is not used, so pushing into it here is dead code.

        } else if (tableTag === 'noTable') {
          console.log(`Variant ${variant.ident} is tagged as noTable, will not be reported`);
          doNotReport.push(variant);
          doNotReportIdents.add(variant.ident);
        }

app/routes/report/variants.js:130

• doNotReport is never read, so this push is dead code and can be removed (the ident Set is sufficient for filtering).

      if (variant?.observedVariantAnnotation?.annotations?.rapidReportTableTag === 'noTable') {
        doNotReport.push(variant);
        doNotReportIdents.add(variant.ident);
        continue;
      }

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[github-actions]

Unit Test Results

    1 files  ±0    64 suites  ±0   4m 5s ⏱️ -8s
659 tests +1  658 ✔️ +1  1 💤 ±0  0 ❌ ±0 
656 runs  +1  655 ✔️ +1  1 💤 ±0  0 ❌ ±0 

Results for commit a6bac45. ± Comparison against base commit 1a3e0a2.