diff --git a/src/cgr_gwas_qc/workflow/scripts/sample_concordance.py b/src/cgr_gwas_qc/workflow/scripts/sample_concordance.py index 982761c8..f01fd346 100755 --- a/src/cgr_gwas_qc/workflow/scripts/sample_concordance.py +++ b/src/cgr_gwas_qc/workflow/scripts/sample_concordance.py @@ -186,7 +186,7 @@ def _discordant_logic(sr: pd.Series) -> bool: ] ): # No metrics so ignore - # Issue 210: If someone is an expected replicates but has no PLINK, GRAF, or KING then these should be flagged as an discordant replicate (True). Before was returning False + # Issue 210: If someone is an expected replicates but has no PLINK, GRAF, or KING then these should be flagged as an discordant replicate (True). Before was returning False return True if pd.notna(sr.PLINK_is_ge_concordance): diff --git a/src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py b/src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py index 9f8e0e8d..eea64c4d 100755 --- a/src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py +++ b/src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py @@ -437,7 +437,6 @@ def _read_intensity(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.Serie .IdatIntensity ) - # TO-ADD: Add a parsing/summary function that returns a Series or DataFrame indexed by Sample_ID