Better error reporting for invalid chromosomes#14
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seppinho merged 1 commit intogenepi:mainfrom Oct 15, 2025
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… covering error case; add test covering missing reference panel. New chrY-fake data is a rename from chr20-phased data using bcftools.
seppinho
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Oct 15, 2025
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Currently, if a user provides a chromosome that is not in the
validChromosomesset fromVcfFileUtil(e.g., chrY), they receive a generic error message:::error:: No valid chromosomes found!(even if other valid chromosomes are submitted). This has caused confusion amongst TOPMed Imputation Server users, who have asked for more specific error reporting.This PR substitutes the error message with
::error:: Invalid chromosome found: <chr>.I have also added two tests based on a code coverage report from the existing test suite:
test-data/data/chrY-fake/, created withbcftoolsfrom existing test data.