feat: Improve handling of unexpected replicates (issue #269) #322
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- Introduces new logic for handling unexpected replicates when one is contaminated. - A new column, unexpected_replicate_status, is added to subject_qc.csv to reflect the updated handling. - Additionally, the description for the unexpected_replicate_status column has been updated in QC_Report_Data_Dictionary.xlsx
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This PR introduces a new methodology for retaining uncontaminated samples in our dataset. Specifically, when we encounter unexpected replicates—where one sample is contaminated and the other is not—this approach allows us to retain the uncontaminated sample while discarding the contaminated one. This code will change the status of the
is_unexpected_replicatefield for the uncontaminated sample. Thus, it changes the reports in theQC_Report.xlsxandQC_Report.docx.A new field has been added to the
subject_qc.csvfile. This field provides a more detailed classification of replicate relationships, including information about retention and contamination. Here's the breakdown of its values:Additionally, we have implemented unit tests to validate the new functionality introduced in the
subject_qc_table.pyscript.Fixes #269