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Validation and Diagnostics

BioFmt diagnostics use stable rule codes and source links so errors can be traced back to format documentation.

Validation Levels

Level What it catches
off No validation
basic Structural errors such as wrong column counts, invalid coordinates, and missing delimiters
strict (default) Everything in basic, plus format-specific checks such as REF/ALT syntax, CIGAR consistency, header declarations, genotype allele bounds, GFF3 references, and duplicate or conflicting IDs

Strict Cross-Field Checks

Format Examples
VCF Sample column count vs header, genotype allele bounds, AD length vs allele count, INFO/FORMAT/FILTER declarations
SAM CIGAR query length vs SEQ length, FLAG conflicts
GFF3 Attribute grammar, Parent and Derives_from resolution, repeated-ID consistency, parent cycles, sequence-region bounds

Diagnostic Actions

Diagnostics expose actions from the VS Code Problems panel and editor quick-fix menu:

  • Open a BioFmt rule explanation.
  • Open the exact upstream specification reference.
  • Copy the rule code and diagnostic summary.
  • Apply safe fixes when BioFmt can make a deterministic, non-destructive edit.

BioFmt intentionally avoids automatic edits that guess scientific data values, reorder records, or delete content.

See the diagnostic rule reference for documented safe fixes and common rule explanations.