BioFmt
BioFmt provides syntax highlighting, intelligent hover tooltips, real-time validation, and interactive previews for 25 genomics, transcriptomics, and proteomics file formats.
Features
- Syntax highlighting for all 25 formats
- Real-time validation with diagnostics shown as you edit
- Hover tooltips for VCF INFO/FORMAT field definitions from file headers
- Interactive previews with virtualized tables handling 200K+ rows, resizable columns, text search, and TSV export
- Automatic format detection via file extension and file content
| Format |
Highlighting |
Validation |
Preview |
| VCF |
Yes |
Yes |
Interactive table with sample data, genotype coloring, expandable rows |
| SAM |
Yes |
Yes |
Alignment table with FLAG decoding, optional tag expansion |
| BED |
Yes |
Yes |
Table with chromosome filter |
| BEDPE |
Yes |
Yes |
Paired-end table with chromosome filter |
| GTF |
Yes |
Yes |
Annotation table with feature/source filter, attribute expansion |
| GFF3 |
Yes |
Yes |
Annotation table with feature/source filter, attribute expansion |
| PSL |
Yes |
Yes |
Alignment table with block visualization |
| PAF |
Yes |
Yes |
Alignment table with tag expansion |
| MAF (alignment) |
Yes |
- |
Multi-alignment block view with nucleotide coloring |
| MAF (mutation) |
Yes |
- |
Mutation table |
| WIG |
Yes |
Yes |
Track plot with downsampling |
| bedGraph |
Yes |
Yes |
Track plot with downsampling |
| narrowPeak |
Yes |
Yes |
Peak table |
| broadPeak |
Yes |
Yes |
Peak table |
| GenBank |
Yes |
- |
Feature outline |
| MTX |
Yes |
- |
Sparse matrix view |
| mzTab |
Yes |
- |
Section-tabbed table |
| MGF |
Yes |
- |
Spectrum list |
| Chain |
Yes |
- |
Chain table with expandable alignment blocks |
| Net |
Yes |
- |
Hierarchical fill/gap tree view |
| GFA |
Yes |
- |
Tabbed view (Segments, Links, Paths, Header) |
| PED |
Yes |
- |
Table |
| MAP |
Yes |
- |
Table |
| GCT |
Yes |
- |
Table |
All preview tables support text search and TSV export.
Installation
- Open VS Code
- Go to Extensions (
Ctrl+Shift+X / Cmd+Shift+X)
- Search for "BioFmt"
- Click Install
Usage
Open a File
Open any supported file format (.vcf, .sam, .bed, etc.). BioFmt automatically activates based on file extension or first-line content.
Open Preview
Click the preview icon in the editor title bar, or use the Command Palette (Ctrl+Shift+P / Cmd+Shift+P) and type BioFmt: Open Preview.
Hover for Field Info
In VCF files, hover over INFO or FORMAT field keys to see their definitions from the file header.
Configuration
| Setting |
Default |
Description |
biofmt.preview.maxLines |
200,000 |
Maximum lines to load in preview |
biofmt.preview.maxBytes |
50 MB |
Maximum file size for preview |
biofmt.preview.downsampleLimit |
200,000 |
Max points in track plots before downsampling |
biofmt.preview.sampleColumnLimit |
10 |
VCF sample columns shown initially |
biofmt.validation.level |
basic |
Validation strictness (off / basic / strict) |
biofmt.validation.maxDiagnostics |
2,000 |
Maximum diagnostics per file |
biofmt.lsp.viewportBufferLines |
500 |
Lines around cursor to validate |
Requirements
License
GPL-3.0 License - see LICENSE for details.
Release Notes
See CHANGELOG for version history.
