Crate rsomics_vcf_expr 

bcftools-style VCF filter-expression parser and per-sample evaluator.

Implements the subset of the bcftools filter language needed for rsomics-vcf-setgt -t q and rsomics-vcf-filter -i/-e:

Supported field references

• FMT/<TAG> / FORMAT/<TAG> — per-sample FORMAT field (numeric)
• INFO/<TAG> — site-level INFO field (numeric or string)
• QUAL — site-level QUAL column (numeric)
• FILTER — site-level FILTER string
• GT — per-sample genotype with special string values: ".", "hom", "het", "ref", "alt", "miss" / "missing"

Operators

• Comparison: < <= > >= == !=
• Logical: && ||
• Parentheses for grouping

Scoped out (exits with error if used):

• Regex operators ~ !~
• Array-index syntax TAG[0]
• Aggregation functions N_PASS(), F_PASS(), SMPL_MAX(), etc.
• Arithmetic + - * / %
• Special fields N_MISSING, F_MISSING, N_ALT, AC, AN, AF

Origin

Independent Rust implementation based on the MIT-licensed bcftools source (filter.c, develop branch) and the VCF 4.3 format specification. Consulted: https://github.com/samtools/bcftools License: MIT OR Apache-2.0 Upstream credit: bcftools https://github.com/samtools/bcftools (MIT)

Re-exports

pub use eval::EvalContext;

pub use eval::EvalError;

pub use eval::SampleResult;

pub use eval::eval_expr;

pub use parse::Expr;

pub use parse::ParseError;

pub use parse::parse_expr;

Modules

eval

Evaluator: runs a parsed Expr against a VCF record line (text representation).

parse

Tokenizer and recursive-descent parser for the filter-expression grammar.