Fix Pacbio read calculation #4748
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diitaz93
reviewed
Dec 3, 2025
| ): | ||
| pass | ||
| def recalculate_sample_reads_pacbio(self, sample_id: str) -> None: | ||
| reads = sum( |
Contributor
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I guess it is not obvious that it is an int
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| reads = sum( | |
| reads: int = sum( |
diitaz93
reviewed
Dec 3, 2025
Comment on lines
123
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| reads: int = 10000 | ||
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| # WHEN updating the reads for the sample | ||
| store.update_sample_reads(internal_id=pacbio_barcoded_sample_internal_id, reads=reads) | ||
| store.update_sample_reads_pacbio(internal_id=pacbio_barcoded_sample_internal_id, reads=reads) | ||
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| # THEN the reads for the sample is updated | ||
| sample: Sample = store.get_sample_by_internal_id(pacbio_barcoded_sample_internal_id) | ||
| assert sample.reads == reads |
Contributor
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I suggest this test(test_update_sample_reads_pacbio) be removed. Seems to me that the new test (test_update_sample_reads_pacbio_not_incremented) covers all the functionality
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Tested by post processing a run name. Recreated the only sample on the sequencing run and after post processing its reads were updated: 
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Description
Closes #4675. Currently, Pacbio samples gets their reads incremented rather than updated. When the same SMRT cell is post processed multiple times (in e.g. deviations), this causes the samples to display the wrong number of reads.
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