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… _build_branch_masks function to streamline gender-based masking. Add robust cutoff calculations for PCA distance filtering in newref_control.py, improving outlier detection and reporting in reference quality control. Update reference QC metrics to include usable chrY bin percentages.
…erence contract functionalities.
…tterns for ignored files and directories.
…, and add compatibility checks in ref_qc.py. Added tests to validate compatibility requirements and ensure consistent behavior across gender branches in the unit tests.
matthdsm
previously approved these changes
Mar 25, 2026
matthdsm
approved these changes
Mar 26, 2026
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