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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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Improve message in summary report for sample fields #125

Closed jmmut closed 6 years ago

jmmut commented 6 years ago

if we validate this file ./bin/vcf_validator -i test/input_files/v4.3/failed/failed_body_sample_003.vcf we get

According to the VCF specification, the input file is not valid Error: Sample #1 does not match the meta specification Number=1 (expected 1 value(s)). This occurs 1 time(s), first time in line 5. Warning: A valid 'reference' entry is not listed in the meta section. This occurs 1 time(s), first time in line 5.

The error doesn't mention which field is the affected. Cange so that this message is displayed

... Error: Sample #1, DS does not match the meta specification Number=1 (expected 1 value(s)). This occurs 1 time(s), first time in line 5. ...

this is written in https://github.com/EBIvariation/vcf-validator/blob/master/src/vcf/record.cpp#L549