What feature is being added or bug is being addressed?
Closes #194. This PR fixes a bug that was causing incorrect submissions to be selected for conflicting variants, in cases where only a single submission was associated with a provided conceptID.
What was your approach?
After Variation IDs that only have one submission associated with a conceptID are identified, these VariationIDs are now being pulled from a df with ONLY ConceptID-associated submissions, rather than a df with all submissions.
What GitHub issue does your pull request address?
194
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please ensure that the updated code logic makes sense and run script from root:
Purpose/implementation Section
What feature is being added or bug is being addressed?
Closes #194. This PR fixes a bug that was causing incorrect submissions to be selected for conflicting variants, in cases where only a single submission was associated with a provided conceptID.
What was your approach?
After Variation IDs that only have one submission associated with a conceptID are identified, these VariationIDs are now being pulled from a df with ONLY ConceptID-associated submissions, rather than a df with all submissions.
What GitHub issue does your pull request address?
194
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please ensure that the updated code logic makes sense and run script from root:
Rscript scripts/select-clinVar-submissions.R --variant_summary data/variant_summary.txt.gz --submission_summary data/submission_summary.txt.gz --conceptID_list data/clinvar_cpg_concept_ids.txt --conflict_res "latest" --outdir resultsIs there anything that you want to discuss further?
No
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