bugfix: exclude samples from relationship checking that are not present in the expected loadable samples #1003
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…nt in the expected loadable samples
bpblanken
commented
Dec 17, 2024
| # Handle case where relation is identified in the | ||
| # pedigree as a "dummy" but is not included in | ||
| # the list of samples to load. | ||
| if other_id not in family.samples: |
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code duplication handled with better for-looping!
bpblanken
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Dec 17, 2024
| class Relation(Enum): | ||
| PARENT = 'parent' | ||
| GRANDPARENT = 'grandparent' | ||
| PARENT_CHILD = 'parent_child' |
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I renamed these for clarity to indicate the bi-directionality.
matren395
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Dec 18, 2024
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really quick - can you explain the Test cases and what the tests are doing before I approve ?
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Yes! So the root issue at play here is parents that are identified in the pedigree but that are not actually real samples present in the callset. We have one test here that ensures we do actually parse those samples as parents. A previous iteration of this code did not... which is why that test exists. The newly added test here checks that the mother ('sample_2') that is parsed from the pedigree does not actually fail the family even if the parent/child relationship is missing from the relatedness check table. |
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okay! now that the tests make sense, lgtm then |
bpblanken
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Jan 7, 2025
* Add service account credentialing (#997) * Add service account credentialing * ruff * feat: Handle parsing empty predicted sex into Unknown (#1000) * Add helper functions for querying `Terra Data Repository` (#998) * Add service account credentialing * ruff * First pass * tests passing * add coverage of bigquery test * change function names * use generators everywhere * bq requirement * resolver * Update sample id name * Build Sex Check Table from TDR Metrics (#999) * refactor: Move feature flags to FeatureFlag enum. (#1002) * refactor: Move feature flags out of environment to their own dataclass * lint: ruff * ruff * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples (#1003) * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples * cleanup * feat: add remap and family loading failures as validation exceptions … (#1005) * feat: add remap and family loading failures as validation exceptions rather than runtime errors * move on * Update write_remapped_and_subsetted_callset_test.py * ruff * feat: Add ability to run tasks dataproc. (#948) * Support gcs dirs in rsync * ws * Add create dataproc cluster task * add dataproc * ruff * requirements * still struggling * Gencode refactor to remove gcs * bump reqs * Run dataproc job * lib * running * merge requirements * Flip'em * Better exception handling * Cleaner approach if less generalizable * write a test * Fix tests * lint * Add test for success * refactor to use a base class... better for adding support for multiple jobs * cleanup * ruff * Fix missing mock * Fix flapping test * pr comments
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This fixes a regression caused by this pr, which modified the relationship checking behavior for parents that are identified in the pedigree but excluded from loading.
Originally we excluded those parental ids from the parsed relationships, which did not work in cases where the parental id helped identify sibling pairs.
This pr preserves the behavior of excluded parents (test case is here), but also allows us to exclude relationships where the sample is not included as loadable in the pedigree (test case is here).