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Bcftools fails in pipeline without being caught #1179

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davmlaw opened this issue Oct 8, 2024 · 0 comments

Milestone

VG4 non-critical

Contributor

davmlaw commented Oct 8, 2024

Delete the FORMAT lines in the header, and import a VCF so you get errors like:

[W::vcf_parse_format_dict2] FORMAT 'AD' at NC_000003.12:10017624 is not defined in the header, assuming Type=String

Then removes it. Pipeline after dies with:

[E::vcf_format] Invalid BCF, the FORMAT tag id=2 at NC_000003.12:10017624 not present in the header
[flush_buffer] Error: cannot write to -
Failed to read from standard input: unknown file type

But this is not caught so pipeline looks like it is still running, rather than error

The text was updated successfully, but these errors were encountered:

davmlaw added this to the VG4 non-critical milestone

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