fix: Handle removal of discordant expected replicates (issue #210) #319
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…ibgfortran issue - Updated bioconductor-illuminaio package in illuminaio.yml to version 0.44.0. - This fixes the previously encountered missing `libgfortran.so.3` dependency. - The newer illuminaio version avoids installing a conflicting version of libgfortran, ensuring proper functionality of R and Rscript needed for the `grouped_median_idat_intensity` rule.
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- In test_sample_qc_table.py and _add_analytic_exclusion function. - This aligns with the data that the function _add_subject_representative receives from the concordance summary. - This ensures consistency with the input data. The column will later be renamed to "Expected Replicate Discordance" in subsequent processing.
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This PR addresses two issues:
sample_qc_table.pyto correctly identify discordant replicates using the actual column name "is_discordant_replicate" from theconcordance summary.csv.remove_rep_discordant=Trueflag inconfig.yml, discordant replicates will be excluded from subject analysis as intended.fixes #210