annonars 0.29.0

Rust template repository
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//! Data structures for (de-)serialization as generated by `prost-build`.

use std::str::FromStr;

pub use crate::pbs::helixmtdb::Record;
use noodles_vcf::record::info::field;

impl Record {
    /// Creates a new `Record` from a VCF record and allele number.
    pub fn from_vcf_allele(
        record: &noodles_vcf::record::Record,
        allele_no: usize,
    ) -> Result<Self, anyhow::Error> {
        let chrom = record.chromosome().to_string();
        let pos: usize = record.position().into();
        let pos = pos as i32;
        let ref_allele = record.reference_bases().to_string();
        let alt_allele = record
            .alternate_bases()
            .get(allele_no)
            .ok_or_else(|| anyhow::anyhow!("no such allele: {}", allele_no))?
            .to_string();
        let num_total = if let Some(Some(field::Value::Integer(num_total))) =
            record.info().get(&field::Key::from_str("AN")?)
        {
            *num_total
        } else {
            anyhow::bail!("missing INFO/AN in HelixMtDb record")
        };
        let num_het = if let Some(Some(field::Value::Integer(num_het))) =
            record.info().get(&field::Key::from_str("AC_het")?)
        {
            *num_het
        } else {
            anyhow::bail!("missing INFO/AC in HelixMtDb record")
        };
        let num_hom = if let Some(Some(field::Value::Integer(num_hom))) =
            record.info().get(&field::Key::from_str("AC_hom")?)
        {
            *num_hom
        } else {
            anyhow::bail!("missing INFO/AC_hom in HelixMtDb record")
        };
        let feature_type = if let Some(Some(field::Value::String(feature))) =
            record.info().get(&field::Key::from_str("FEATURE")?)
        {
            feature.to_string()
        } else {
            anyhow::bail!("missing INFO/FEATURE in HelixMtDb record")
        };
        let gene_name = if let Some(Some(field::Value::String(gene_name))) =
            record.info().get(&field::Key::from_str("GENE")?)
        {
            gene_name.to_string()
        } else {
            anyhow::bail!("missing INFO/GENE in HelixMtDb record")
        };

        Ok(Record {
            chrom,
            pos,
            ref_allele,
            alt_allele,
            num_total,
            num_het,
            num_hom,
            feature_type,
            gene_name,
        })
    }
}