Fix cnv_discordant_read_calls: raise ValueError when no data found #781
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This looks good, thank you @Jiya873. I am going to shadow this PR to enable the checks. If you updated |
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Additional details and impacted files@@ Coverage Diff @@
## master #781 +/- ##
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- Coverage 96.13% 96.07% -0.06%
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Files 47 47
Lines 4683 4689 +6
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+ Hits 4502 4505 +3
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Hi @jonbrenas, I had indeed forgotten to push the updated test_cnv_data.py earlier. I've just pushed the changes now. Please let me know if everything looks good or if further updates are needed. |
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Thank you @Jiya873. It looks like the tests don't like your monkeypatching. I will try to look at what seems to be the problem ...if you don't beat me to it. |
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Not sure what state this PR is in? |
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I think it has been abandoned. |
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Thanks @jonbrenas . If there's no response after a short time (say, September) then I guess we'll close this. This PR can always be resurrected, if needs be. |
This pull request addresses issue #777 where calling
cnv_discordant_read_callswith absent data was causing anIndexErrorinstead of the expectedValueError. The changes include:Refactoring
cnv_discordant_read_calls:The empty-data check is now moved outside the inner loop that iterates over the sample sets. If no dataset is found for a contig (or across all contigs), a ValueError is raised with an informative message.
Updated Tests:
The relevant tests in
test_cnv_data.pyhave been leveraged to confirm that the expectedValueErroris raised in cases where data is absent (e.g., for non-existent sample sets or contigs).These changes ensure that the API behaves more predictably and makes debugging easier when data is missing.