Handle "reads per cell" in 10xGenomics metrics file being non-integer value when reporting multiplexed QC #1011
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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:compared with:
Without the bugfix the QC reporting fails as the
SampleQCReporter.get_10x_value()
method inqc/reporting.py
encounters an untrapped error attempting to format a non-integer value for the10x_reads_per_cell
field. The fix allows for non-integer values specifically for this field to be return as-is as string instead.