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Diagnostic Rule Reference

BioFmt diagnostics use stable rule codes. Use the editor quick-fix menu on a diagnostic to open this rule reference, open the upstream specification, copy details, or apply a safe fix when one exists.

Common Rules

GFF3_MISSING_VERSION

GFF3 files must declare the version before feature records, comments, or FASTA content.

Required first line:

##gff-version 3

Safe fix: BioFmt can insert ##gff-version 3 at the top of the file. This edit does not change feature coordinates, attributes, or sequence content.

Specification: GFF3 version directive

Other Rules

For other diagnostics, use BioFmt: Open specification from the quick-fix menu to jump to the source format document. Use BioFmt: Copy details to copy the rule code, summary, and exact specification URL into bug reports or notes.