bugfix: retrieve additional missing data from QC_Report.xlsx
#307
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- Removed "IdatsInProjectDir" from _SAMPLE_QC_COLUMNS and QC_Report.xlsx. - The "IdatsInProjectDir" column was empty in QC_Report.xlsx because it is not present in sample_qc.csv. - The equivalent column "is_missing_idats" is already included in QC_Report.xlsx, containing the same information from cgr_sample_sheet.csv. - Therefore, the "IdatsInProjectDir" column has been removed to avoid redundancy.
Removes "Expected Replicate" from _SAMPLE_QC_COLUMNS and thus the QC_Report.xlsx. It duplicates the more informative "Replicate IDs" column in the QC_Report.xlsx
- Introduces functionality to calculate the total number of QC issues
present in a sample.
- Addresses missing data in the "Count_of_QC_Issue" column of
QC_Report.xlsx.
- Calculates the number of "TRUE" occurrences in five boolean columns:
"Low Call Rate",
"Contaminated",
"Expected Replicate Discordance",
"Unexpected Replicate",
and "Sex Discordant".
- Fills in missing data for "Sample Pass QC" column in QC_Report.xlsx.
- Populates the column with a boolean value indicating if a sample passed all QC metrics:
"Low Call Rate",
"Contaminated",
"Expected Replicate Discordance",
"Unexpected Replicate",
and "Sex Discordant".
- A sample passes QC if `Count_of_QC_Issue` is 0 (no QC issues).
- Otherwise, the sample fails and the column is set to False.
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This PR fixes missing data in the SAMPLE_QC tab of the
QC_Report.xlsx. In particular, it implements the logic to capture data for the "Count_of_QC_Issue" and "Sample Pass QC" columns. It also removes redundant columns "Expected Replicate" and "IdatsInProjectDir" from the tab.Fixes #306