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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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Text report #159

Closed srbcheema1 closed 5 years ago

srbcheema1 commented 5 years ago

This PR is to add functionality of writing text-report in assembly_checker tool. this report will be similar like the text report in vcf-validator.

cyenyxe commented 5 years ago

the reports are always written in the same folder as the input files, or current one if using stdin. a -o parameter would be useful as in the main validator.

+1

it tries to search angle-bracketed IDs from the CHROM column as-is in the fasta file.

I haven never seen those in a FASTA file, but if that is what the VCF input looks like, then that is what is needs to be checked. The only field that I can recall has a special meaning for angle brackets is ALT (for symbolic alternates).

in the "valid" report, the header is not written, so the output is not a valid VCF. of course, we are skipping the header entirely so we might need to make some structure changes

Maybe we should disable the "valid" report for now in order to get this PR merged, and enable it in a future one.