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Handle "reads per cell" in 10xGenomics metrics file being non-integer value when reporting multiplexed QC #1011

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Jan 9, 2025

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Handles the special case of the "reads per cell" value in a cellranger multi metrics_summary.csv file not being an integer when reporting 10x Genomics multiplexed statistics.

For example if no cells were assigned to a multiplexed sample then the metrics_summary.csv file might contain the line:

Cells,Gene Expression,,,Mean reads per cell,---

compared with:

Cells,Gene Expression,,,Mean reads per cell,"20,614"

Without the bugfix the QC reporting fails as the SampleQCReporter.get_10x_value() method in qc/reporting.py encounters an untrapped error attempting to format a non-integer value for the 10x_reads_per_cell field. The fix allows for non-integer values specifically for this field to be return as-is as string instead.

@pjbriggs pjbriggs merged commit e03496f into devel Jan 9, 2025
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@pjbriggs pjbriggs deleted the 10x-cellplex-qc-reporting-no-reads-in-cell branch January 9, 2025 11:05
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