Fix missing groups for included strains #1000
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1000 +/- ##
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Coverage 59.24% 59.24%
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Files 50 50
Lines 6266 6267 +1
Branches 1588 1588
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+ Hits 3712 3713 +1
Misses 2292 2292
Partials 262 262 ☔ View full report in Codecov by Sentry. |
victorlin
approved these changes
Jul 6, 2022
tests/functional/filter/cram/subsample-group-by-without-force-included-strains.t
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Fixes a subtle bug when grouping with subsampled max sequences and force-included strains that could potentially be considered for subsampling. In the first pass through the metadata, we remove force-included strains from consideration for subsampling. However, we do not similarly remove these strains in the second pass through the metadata. If these strains have not been filtered earlier, we consider them for subsampling in the second pass and look for a queue with their group-by attributes. Since queue creation depends on the group attributes we find in the first pass, it is possible for the group attributes of the force-included strains to not have a queue. This commit adds a functional test to recreate the bug (originally discovered in the ncov workflow) and updates the logic in the second pass to remove force-included strains prior to building subsampling groups.
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Description of proposed changes
Fixes a subtle bug when grouping with subsampled max sequences and
force-included strains that could potentially be considered for
subsampling. In the first pass through the metadata, we remove
force-included strains from consideration for subsampling. However, we
do not similarly remove these strains in the second pass through the
metadata. If these strains have not been filtered earlier, we consider
them for subsampling in the second pass and look for a queue with their
group-by attributes. Since queue creation depends on the group
attributes we find in the first pass, it is possible for the group
attributes of the force-included strains to not have a queue.
This commit adds a functional test to recreate the bug (originally
discovered in the ncov workflow) and updates the logic in the second
pass to remove force-included strains prior to building subsampling
groups.
Related issues
Testing