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fix: Update column names to "is_discordant_replicate"
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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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jaamarks committed Sep 6, 2024
1 parent 408550c commit 673254b
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Showing 2 changed files with 2 additions and 2 deletions.
2 changes: 1 addition & 1 deletion src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py
Original file line number Diff line number Diff line change
Expand Up @@ -534,7 +534,7 @@ def _add_analytic_exclusion(
exclusion_criteria["is_contaminated"] = "Contamination"

if remove_rep_discordant:
exclusion_criteria["Expected Replicate Discordance"] = "Replicate Discordance"
exclusion_criteria["is_discordant_replicate"] = "Replicate Discordance"

sample_qc["analytic_exclusion"] = sample_qc.reindex(exclusion_criteria.keys(), axis=1).any(
axis=1
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2 changes: 1 addition & 1 deletion tests/workflow/scripts/test_sample_qc_table.py
Original file line number Diff line number Diff line change
Expand Up @@ -254,7 +254,7 @@ def fake_sample_qc() -> pd.DataFrame:
"is_cr1_filtered",
"is_cr2_filtered",
"is_contaminated",
"Expected Replicate Discordance",
"is_discordant_replicate",
]
data = [
("SP00001", "SB00001", False, False, 0.99, False, False, False, False),
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