noodles_vcf/variant/record_buf/

builder.rs

//! VCF record builder.

use noodles_core::Position;

use super::{AlternateBases, Filters, Ids, Info, RecordBuf, Samples};

/// A VCF record builder.
#[derive(Debug, PartialEq)]
pub struct Builder {
    reference_sequence_name: String,
    variant_start: Option<Position>,
    ids: Ids,
    reference_bases: String,
    alternate_bases: AlternateBases,
    quality_score: Option<f32>,
    filters: Filters,
    info: Info,
    samples: Samples,
}

impl Builder {
    /// Sets the reference sequence name.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf as vcf;
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_reference_sequence_name("sq0")
    ///     .build();
    ///
    /// assert_eq!(record.reference_sequence_name(), "sq0");
    /// ```
    pub fn set_reference_sequence_name<N>(mut self, reference_sequence_name: N) -> Self
    where
        N: Into<String>,
    {
        self.reference_sequence_name = reference_sequence_name.into();
        self
    }

    /// Sets the variant start position.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_core::Position;
    /// use noodles_vcf as vcf;
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_variant_start(Position::MIN)
    ///     .build();
    ///
    /// assert_eq!(record.variant_start(), Some(Position::MIN));
    /// ```
    pub fn set_variant_start(mut self, position: Position) -> Self {
        self.variant_start = Some(position);
        self
    }

    /// Sets a list of IDs.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::{self as vcf, variant::record_buf::Ids};
    ///
    /// let ids: Ids = [String::from("nd0")].into_iter().collect();
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_ids(ids.clone())
    ///     .build();
    ///
    /// assert_eq!(record.ids(), &ids);
    /// ```
    pub fn set_ids(mut self, ids: Ids) -> Self {
        self.ids = ids;
        self
    }

    /// Sets the reference bases.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf as vcf;
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_reference_bases("A")
    ///     .build();
    ///
    /// assert_eq!(record.reference_bases(), "A");
    /// ```
    pub fn set_reference_bases<B>(mut self, reference_bases: B) -> Self
    where
        B: Into<String>,
    {
        self.reference_bases = reference_bases.into();
        self
    }

    /// Sets the alternate bases.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::{self as vcf, variant::record_buf::AlternateBases};
    ///
    /// let alternate_bases = AlternateBases::from(vec![String::from("C")]);
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_alternate_bases(alternate_bases.clone())
    ///     .build();
    ///
    /// assert_eq!(record.alternate_bases(), &alternate_bases);
    /// ```
    pub fn set_alternate_bases(mut self, alternate_bases: AlternateBases) -> Self {
        self.alternate_bases = alternate_bases;
        self
    }

    /// Sets the quality score.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf as vcf;
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_quality_score(13.0)
    ///     .build();
    ///
    /// assert_eq!(record.quality_score(), Some(13.0));
    /// ```
    pub fn set_quality_score(mut self, quality_score: f32) -> Self {
        self.quality_score = Some(quality_score);
        self
    }

    /// Sets the filters.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::{self as vcf, variant::record_buf::Filters};
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_filters(Filters::pass())
    ///     .build();
    ///
    /// assert!(record.filters().is_pass());
    /// ```
    pub fn set_filters(mut self, filters: Filters) -> Self {
        self.filters = filters;
        self
    }

    /// Sets additional information.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::{
    ///     self as vcf,
    ///     variant::{
    ///         record::info::field::key,
    ///         record_buf::{info::field::Value, Info},
    ///     },
    /// };
    ///
    /// let info: Info = [
    ///     (String::from(key::SAMPLES_WITH_DATA_COUNT), Some(Value::Integer(3))),
    ///     (String::from(key::ALLELE_FREQUENCIES), Some(Value::from(vec![Some(0.5)]))),
    /// ]
    /// .into_iter()
    /// .collect();
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_info(info.clone())
    ///     .build();
    ///
    /// assert_eq!(record.info(), &info);
    /// ```
    pub fn set_info(mut self, info: Info) -> Self {
        self.info = info;
        self
    }

    /// Sets the list of genotypes.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::{
    ///     self as vcf,
    ///     variant::{
    ///         record::samples::keys::key,
    ///         record_buf::{samples::{sample::Value, Keys}, Samples},
    ///     },
    /// };
    ///
    /// let keys: Keys = [
    ///     String::from(key::GENOTYPE),
    ///     String::from(key::CONDITIONAL_GENOTYPE_QUALITY),
    /// ].into_iter().collect();
    ///
    /// let samples = Samples::new(
    ///     keys,
    ///     vec![vec![Some(Value::from("0|0")), Some(Value::from(13))]],
    /// );
    ///
    /// let record = vcf::variant::RecordBuf::builder()
    ///     .set_samples(samples.clone())
    ///     .build();
    ///
    /// assert_eq!(record.samples(), &samples);
    /// ```
    pub fn set_samples(mut self, samples: Samples) -> Self {
        self.samples = samples;
        self
    }

    /// Builds a VCF record.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf as vcf;
    /// let record = vcf::variant::RecordBuf::builder().build();
    /// ```
    pub fn build(self) -> RecordBuf {
        RecordBuf {
            reference_sequence_name: self.reference_sequence_name,
            variant_start: self.variant_start,
            ids: self.ids,
            reference_bases: self.reference_bases,
            alternate_bases: self.alternate_bases,
            quality_score: self.quality_score,
            filters: self.filters,
            info: self.info,
            samples: self.samples,
        }
    }
}

impl Default for Builder {
    fn default() -> Self {
        Self {
            reference_sequence_name: String::new(),
            variant_start: Some(Position::MIN),
            ids: Ids::default(),
            reference_bases: String::new(),
            alternate_bases: AlternateBases::default(),
            quality_score: None,
            filters: Filters::default(),
            info: Info::default(),
            samples: Samples::default(),
        }
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::variant::record::AlternateBases as _;

    #[test]
    fn test_default() {
        let record = Builder::default();

        assert!(record.reference_sequence_name.is_empty());
        assert_eq!(record.variant_start, Some(Position::MIN));
        assert!(record.ids.as_ref().is_empty());
        assert!(record.reference_bases.is_empty());
        assert!(record.alternate_bases.is_empty());
        assert!(record.quality_score.is_none());
        assert!(record.filters.as_ref().is_empty());
        assert!(record.info.as_ref().is_empty());
        assert!(record.samples.is_empty());
    }
}