libbiosyntax

User guide

This guide covers supported formats, the highlighting model, class metadata, and example CLIs.

Supported formats

• FASTA
• FASTA nucleotide scheme: fasta-nt
• FASTA high-contrast nucleotide scheme: fasta-hc
• FASTA Clustal amino-acid scheme: fasta-clustal
• FASTA hydrophobicity scheme: fasta-hydro / fasta-hydrophobicity
• FASTA Taylor amino-acid scheme: fasta-taylor
• FASTA Zappo amino-acid scheme: fasta-zappo
• FASTA ORF mode: fasta-orf
• FASTQ
• SAM
• VCF
• BED
• GTF
• GFF
• PDB
• CLUSTAL alignment
• FASTA index / .fai
• SAM flagstat
• WIG / bedGraph-like lines

biosyn_guess_format_from_path() recognizes BioSyntax-style FASTA scheme extensions such as .faa/.fastaa, .fas/.mfa, .fastahydro, .fastaylor, and .fastza.

Highlighting details

libbiosyntax returns semantic token classes rather than final colors only. Important token families include:

• individual nucleotide and IUPAC ambiguity classes: nt_a, nt_c, nt_g, nt_t, nt_u, nt_n, nt_r, nt_y, nt_s, nt_w, nt_m, nt_k, nt_d, nt_b, nt_v, nt_h, and nt_x;
• high-contrast nucleotide classes for fasta-hc;
• amino-acid classes for Clustal, Zappo, Taylor, and hydrophobicity schemes;
• ORF start, coding-region, and stop-codon classes;
• SAM CIGAR and quality classes;
• SAM header tags for @HD, @SQ, @RG, @PG, and comments;
• VCF meta-line attributes, INFO attributes, FORMAT fields, sample delimiters, missing genotype values, numbers, quoted strings, URLs, and symbolic alleles;
• BED/GTF/GFF feature, strand, score-gradient, and attribute classes;
• PDB record, residue, chain, coordinate, occupancy, temperature-factor, and element classes;
• FASTA index column classes;
• SAM flagstat passed/failed counts and percentages;
• WIG fixedStep and variableStep state-aware value classes.

Class metadata and default colors

The C library includes built-in BioSyntax-inspired class metadata. No external theme file is required at runtime. Applications can retrieve class names, scopes, ANSI SGR fragments, foreground colors, background colors, and font style hints:

const char *biosyn_class_name(biosyn_class_t class_id);
const char *biosyn_class_scope(biosyn_class_t class_id);
const char *biosyn_class_ansi_sgr(biosyn_class_t class_id);
const char *biosyn_class_default_foreground(biosyn_class_t class_id);
const char *biosyn_class_default_background(biosyn_class_t class_id);
const char *biosyn_class_default_font_style(biosyn_class_t class_id);

biosyn_class_info_t info;
int ok = biosyn_class_info(BIOSYN_CLASS_NT_A, &info);

Use biosyn_class_count() to iterate over all token classes. The metadata API is the supported way to build editor themes, GUI styles, or binding-level lookup tables.

CLI examples

bcat is the simplest ANSI-rendering example. It is a small POSIX C program for plain text input:

make examples
build/bcat -f vcf sample.vcf
build/bcat -f fasta-zappo proteins.fa
build/bcat sample.fa

biocat is the HTSlib-backed example for compressed and binary bioinformatics files:

make biocat
build/biocat sample.vcf.gz
build/biocat sample.bam

biocat reads input through HTSlib, including .gz/.bgz text, BAM, CRAM, and BCF. Binary alignment and variant files are converted to SAM or VCF text in the CLI before highlighting.

Build both examples with:

make examples
make biocat

Only biocat is linked with HTSlib. Install HTSlib development headers and library before running make biocat. The core library itself has no HTSlib dependency.

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