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PGScatalog / pgscatalog_utils

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files
Apache License 2.0
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More informative error messages #36

Open smlmbrt opened 1 year ago

smlmbrt commented 1 year ago

Hard to debug certain error messages for users as the assertions don't list the problematic variants (e.g. duplicate IDs, https://github.com/PGScatalog/pgsc_calc/issues/72#issue-1513968684). Should consider adding list of scoring files/variants that are causing the breakage

Relevant code snippet: https://github.com/PGScatalog/pgscatalog_utils/blob/5bd8a2b7bce9d651e4233650cced8ce577a06539/pgscatalog_utils/match/combine_matches.py#L39-L48

smlmbrt commented 1 year ago

I think here we need to output: ['accession', 'ID', [list of affected scoring file row_nr]] that way we can grep the relevant rows of pvar and scoring file to see what's wrong