Better error reporting for invalid chromosomes #14

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Merged

seppinho merged 1 commit into genepi:main from statgen:ux-better-error-on-invalid-chromosome

Oct 15, 2025

Merged

Better error reporting for invalid chromosomes #14

Improve error reporting when an invalid chromosome is found; add test…

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5 errors and 7 warnings

No genotypes found in the VCF file. It appears the file contains only the header.

Your upload data contains chromosome 'chr20'. This is not a valid hg19 encoding. Please ensure that your input data is build hg19 and chromosome is encoded as '20'.

The provided VCF file is malformed. Error during index creation: Input file is not in valid block compressed format., for input source: /home/runner/work/imputationserver-utils/imputationserver-utils/test-data/data/unorderd/minimac_test.50.vcf.gz

Unable to parse reference panel: this-path/does-not-exist.json (No such file or directory)

Invalid chromosome found: Y

Uploaded data is hg19 and reference is hg38.

Skip allele frequency check.

Uploaded data is hg19 and reference is hg38.

Uploaded data is hg38 and reference is hg19.

Skip allele frequency check.

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Better error reporting for invalid chromosomes #14

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Better error reporting for invalid chromosomes #14

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