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Fix AVITI readmasks#468

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kedhammar merged 5 commits intoNationalGenomicsInfrastructure:masterfrom
kedhammar:aviti-readmasks
Mar 11, 2025
Merged

Fix AVITI readmasks#468
kedhammar merged 5 commits intoNationalGenomicsInfrastructure:masterfrom
kedhammar:aviti-readmasks

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@kedhammar
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Trying to create readmasks from the LIMS run recipe string (which is 0-0 / 0-0-0-0 for PhiX and Controls respectively) causes them to get no reads at all, which makes sense.

For recipes whose read lengths are set to 0, just set the read mask to include everything I guess?

…ads that are shorter than the cycles used BUT assume recipes that are zero are intended to be full-length reads
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codecov bot commented Mar 11, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 28.34%. Comparing base (dbad368) to head (2fc250f).
Report is 10 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #468      +/-   ##
==========================================
- Coverage   28.35%   28.34%   -0.01%     
==========================================
  Files          37       37              
  Lines        5544     5545       +1     
==========================================
  Hits         1572     1572              
- Misses       3972     3973       +1     

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@kedhammar kedhammar requested a review from ssjunnebo March 11, 2025 11:44
@kedhammar
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The mypy failure is a CI issue which is patched in #467

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👍

@kedhammar kedhammar merged commit 61f7541 into NationalGenomicsInfrastructure:master Mar 11, 2025
@kedhammar kedhammar deleted the aviti-readmasks branch March 17, 2025 12:12
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