Better error message for gene_cnv_frequencies() if no cohorts are available for the given sample selection parameters #668
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alimanfoo
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Thanks @jonbrenas, happy to merge this now, assuming there will be some refactoring later via #665 to bring handling of these errors in all frequencies functions into a single location.
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* Moving cnv frequencies functions to their own file * Changes that should help with legacy tests * Stuck on creating tests. * Adding some tests for CNV freqs * Made the same change as in #668 * Added check_type * Added a test for max_coverage_variance in the advanced version * Added a test for max_coverage_variance for the normal version * Update malariagen_data/anoph/cnv_frq.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Removes the old functions in anopheles.py * Linting * Updated some legacy tests * Updated doc, I think * Added more tests and a nobs_mode parameter * Apply suggestions from code review * Finished the merge * Removed an unused function in test_ag3.py --------- Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
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Resolves #667.
It should pass all tests, mostly because there are no CNV frequencies tests yet.