bugfix: is_unexpected_replicate data missing in QC_Report.xlsx
#304
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The `QC_Report.xlsx` was missing data for the `is_unexpected_replicate` column in the `SAMPLE_QC`, `SAMPLE_CONCORDANCE`, and `SUBJECT_QC` sheets. This issue arose from a column name change in commit `825c8a57e2003e8c5a55aded8759584f950752cc`, where `Unexpected Replicate` was renamed to `is_unexpected_replicate`. The renaming caused blank entries due to the reindexing step in `qc_report_tables.py`. During reindexing, `is_unexpected_replicate` was not found in the DataFrame because of the earlier renaming, leading to NaN values. Pandas docs state, "By default, values in the new index that do not have corresponding records in the DataFrame are assigned NaN." To resolve this, the column names have been reverted to their original title, `Unexpected Replicate`.
- Renamed parameter `sample_qc_csv` to `subject_qc_csv` to better reflect its intended use.
…s Removed" We noticed a discrepancy in the terminology we are using in Table 4a. It uses "Expected Duplicates Removed", while other parts of the pipeline uses "Expected Replicates". So we updated Table 4a to "Expected Replicates Removed" for consistency throughout the pipeline.
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This resolves the issue of missing data for the
is_unexpected_replicatecolumn in theSAMPLE_QC,SAMPLE_CONCORDANCE, andSUBJECT_QCsheets ofQC_Report.xlsx.The column name was changed from
Unexpected Replicatetois_unexpected_replicatein commit825c8a57e2003e8c5a55aded8759584f950752cc, causing blank entries due to the reindexing step inqc_report_tables.py. Reverting the column name toUnexpected Replicatefixes this issue.Additionally
Refactoring + minor fixes related to the QC_Report.
Fixes #303