BioFmt
Syntax highlighting, spec-referenced validation, and interactive previews for 27 genomics, transcriptomics, and proteomics formats in VS Code — including indexed and binary files.
Features
Syntax Highlighting
TextMate grammars for all 27 formats with distinct coloring for field types, headers, and data regions. Works in any VS Code color theme.
Spec-Referenced Diagnostics
Every diagnostic carries a rule code and a clickable link to the relevant format specification. Hover a squiggle to see which rule was violated and jump directly to the VCF v4.4, SAM v1, GFF3, or BED spec.
Three validation levels:
| Level |
What it catches |
| off |
No validation |
| basic |
Structural errors: wrong column count, non-integer coordinates, missing delimiters |
| strict (default) |
Everything in basic, plus: REF/ALT format, CIGAR syntax, FILTER/FORMAT header declarations, genotype allele bounds, CIGAR vs SEQ length, GFF3 Parent resolution, and more |
Cross-field validation (strict mode) catches the errors that break pipelines:
- VCF: sample column count vs header, genotype allele index bounds, AD length vs allele count, INFO/FORMAT/FILTER header declarations
- SAM: CIGAR query length vs SEQ length, FLAG bit conflicts (unmapped + properly paired)
- GFF3: Parent attribute resolution (missing/duplicate IDs)
Interactive Previews
Virtualized tables handle 200K+ rows with search, column sorting, drag-resizable columns, and TSV export. Format-specific views include:
- VCF: color-coded INFO/FORMAT fields, sample hover tooltips, FILTER badges, chromosome sorting
- SAM/BAM: FLAG decoding, tag parsing, alignment details
- WIG/bedGraph: interactive track plots with downsampling
- MGF: spectrum plots
- GenBank: feature outline view
- GFA: tabbed segments/links/paths view
- FASTA: per-base coloring (A/T/G/C/N)
- FASTQ: quality heatmap with Phred score color gradient
Indexed & Binary File Support
Open compressed and indexed files directly — no decompression needed:
.vcf.gz + .tbi/.csi (tabix).bed.gz + .tbi/.csi (tabix).gff3.gz + .tbi/.csi (tabix).bam + .bai/.csi
Navigate by genomic region with the built-in region bar. Type chr1:1000000-2000000 for a range, chr1:500000 for a 10kb window around a position, or select a chromosome from the dropdown.
Workspace-Wide Lint
Validate all bioinformatics files across your workspace — not just the ones you have open. Diagnostics appear in the VS Code Problems panel, making it easy to clean up datasets or audit file collections.
Enable with biofmt.workspace.enableLint. Off by default.
| Format |
Extensions |
Indexed |
| VCF |
.vcf |
.vcf.gz + .tbi/.csi |
| SAM / BAM |
.sam |
.bam + .bai/.csi |
| BED |
.bed |
.bed.gz + .tbi/.csi |
| BEDPE |
.bedpe |
|
| GTF |
.gtf |
|
| GFF3 |
.gff, .gff3 |
.gff3.gz + .tbi/.csi |
| FASTA |
.fasta, .fa, .fna, .ffn, .faa, .frn |
|
| FASTQ |
.fastq, .fq |
|
| PSL |
.psl |
|
| PAF |
.paf |
|
| WIG |
.wig |
|
| bedGraph |
.bedGraph, .bdg |
|
| narrowPeak |
.narrowPeak |
|
| broadPeak |
.broadPeak |
|
Specialized previews (no validation)
MAF (alignment), MAF (mutation), GenBank, MTX (Matrix Market), mzTab, MGF, Chain, Net, GFA
Generic preview
PED, MAP, GCT, HTSeq, Salmon, Kallisto
Installation
Search BioFmt in the VS Code Extensions panel (Ctrl+Shift+X / Cmd+Shift+X) and click Install.
Usage
- Open any supported file in VS Code
- Click the preview icon in the editor title bar, or run BioFmt: Open Preview from the Command Palette (
Ctrl+Shift+P / Cmd+Shift+P)
- Indexed/binary files (
.vcf.gz, .bam, etc.) open directly with a region navigator — type a coordinate to query
- Hover over INFO or FORMAT keys in VCF data rows to see field definitions and spec references
Configuration
Validation
| Setting |
Default |
Description |
biofmt.validation.level |
strict |
Validation strictness: off, basic, or strict |
biofmt.validation.maxDiagnostics |
2000 |
Maximum diagnostics reported per file |
biofmt.lsp.viewportBufferLines |
500 |
Number of lines around the cursor to validate |
Previews
| Setting |
Default |
Description |
biofmt.preview.maxLines |
200000 |
Maximum lines loaded in preview |
biofmt.preview.maxBytes |
52428800 |
Maximum file size in bytes for preview (50 MB) |
biofmt.preview.sampleColumnLimit |
10 |
VCF sample columns shown initially |
biofmt.preview.downsampleLimit |
200000 |
Track plot point limit before downsampling |
biofmt.preview.maxRegionRecords |
10000 |
Maximum records per region query (indexed files) |
Workspace Lint
| Setting |
Default |
Description |
biofmt.workspace.enableLint |
false |
Validate all bioinformatics files in the workspace |
biofmt.workspace.maxFiles |
100 |
Maximum number of files to validate |
biofmt.workspace.maxFileSizeMB |
10 |
Maximum file size (MB) for workspace validation |
Requirements
VS Code 1.85.0 or higher.
License
GPL-3.0 — see LICENSE.
Changelog
See CHANGELOG.
