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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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Add locus (e.g. chr:start-end) to warning/error log along line number #152

Closed ambarrio closed 4 years ago

ambarrio commented 5 years ago

This is probably more of a feature request than any issue.

It would be a nice to have as it would facilitate extracting lines from a VCF with e.g. tabix rather than counting lines.

Line 184: Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=101,0. It must derive its number of values from the ploidy of GT (if present)
Line 319: Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=90,0. It must derive its number of values from the ploidy of GT (if present)
Line 465: Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=75,0. It must derive its number of values from the ploidy of GT (if present)

to 

Line 184 (chrA:startA-endA): Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=101,0. It must derive its number of values from the ploidy of GT (if present)
Line 319 (chrB:startB-endB): Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=90,0. It must derive its number of values from the ploidy of GT (if present)
Line 465 (chrC:startC-endC): Sample #1, field PL does not match the meta specification Number=G (expected 3 value(s)). PL=75,0. It must derive its number of values from the ploidy of GT (if present)
tcezard commented 4 years ago

This is not really needed at this time: closing the issue