cyanea-io

Unified file format parsing for bioinformatics. Each parser is behind a feature flag to keep the dependency tree minimal.

What's Inside

• CSV -- metadata extraction, preview
• VCF -- variant parsing into cyanea-omics::Variant, streaming stats
• BED -- BED3-BED6 records, interval conversion, statistics
• BEDPE -- paired-end intervals with inter/intra-chromosomal stats
• GFF3 -- hierarchical Gene/Transcript/Exon assembly with coordinate conversion
• GTF -- GFF2 format with gene_id/transcript_id hierarchy
• SAM -- full record parsing, flag helpers, paired-end stats, pileup generation
• BAM -- BGZF-compressed binary alignment parsing
• CRAM -- reference-based alignment format via noodles
• BCF -- BCF2.1 binary VCF parsing
• BLAST -- tabular output (-outfmt 6/7) parsing
• MAF -- Multiple Alignment Format (UCSC/LAST/minimap2)
• GenBank -- flat file parsing (multi-record, features table)
• bigWig/bigBed -- Kent binary formats with B+ tree and R-tree index
• Parquet -- columnar storage for variants, intervals, and expression matrices with predicate pushdown

Quick Start

[dependencies]
cyanea-io = { version = "0.1", features = ["vcf", "bed", "sam"] }

use cyanea_io::{vcf::vcf_stats, bed::parse_bed, sam::parse_sam};

let stats = vcf_stats("variants.vcf").unwrap();
println!("{} variants, {} SNVs", stats.variant_count, stats.snv_count);

let regions = parse_bed("regions.bed").unwrap();
let alignments = parse_sam("reads.sam").unwrap();

Feature Flags

Modules

See Also

• API Reference
• Usage Guide
• Internal Architecture
• Workspace Architecture
• Build Guide