feat: Improve handling of discordant expected replicates (issue #324) #327
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- Previously, both samples in a discordant expected replicate pair were discarded. Now, if one sample has low call rate or is flagged as contaminated, and the other does not, the high-quality sample is retained. This helps preserve subject data when one sample is compromised. - Updated unit tests to cover the new functionality.
- We need to adjust the other test parameters impacted by the changes in how we handle discordant expected replicates, as well as the addition of new entries in the `fake_sample_qc` DataFrame.
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This PR creates a new function
_retain_valid_discordant_replicatesto the scriptsample_qc_table.py, which helps us retain additional subjects in specific cases. Previously, both samples in a discordant expected replicate pair were discarded. Now, if one sample has low call rate or is flagged as contaminated, and the other does not, the high-quality sample is retained. This helps preserve subject data when one sample is compromised.Additionally, we updated the unit tests in
test_sample_qc_table.pyto cover the new functionality.Fixes #324