1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262
//! BCF record and fields.
mod convert;
mod filters;
mod genotypes;
mod info;
pub(crate) mod value;
pub(crate) use self::value::Value;
pub use self::{filters::Filters, genotypes::Genotypes, info::Info};
use std::io;
use noodles_vcf as vcf;
/// A chromosome ID.
pub type ChromosomeId = usize;
/// A BCF record.
#[derive(Clone, Debug, PartialEq)]
pub struct Record {
chrom: ChromosomeId,
pos: vcf::record::Position,
rlen: i32,
qual: Option<vcf::record::QualityScore>,
id: vcf::record::Ids,
pub(crate) r#ref: vcf::record::ReferenceBases,
pub(crate) alt: vcf::record::AlternateBases,
filter: Filters,
info: Info,
genotypes: Genotypes,
}
impl Record {
/// Returns the chromosome ID of the record.
///
/// The chromosome ID represents an index in the contig string map, which associates an ID (by
/// position) with a contig record in the VCF header (by name). That is, to get the associated
/// contig record in the VCF header, the contig string map must first be queried by position to
/// find the chromosome name, and then the contigs in the VCF header can be queried by name.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert_eq!(record.chromosome_id(), 0);
/// ```
pub fn chromosome_id(&self) -> ChromosomeId {
self.chrom
}
pub(crate) fn chromosome_id_mut(&mut self) -> &mut ChromosomeId {
&mut self.chrom
}
/// Returns the start position of this record.
///
/// Despite the BCF format using 0-based positions, this normalizes the value as a 1-based
/// position.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert_eq!(i32::from(record.position()), 1);
/// ```
pub fn position(&self) -> vcf::record::Position {
self.pos
}
/// Returns a mutable reference to the start position.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// use noodles_vcf::record::Position;
///
/// let mut record = bcf::Record::default();
/// *record.position_mut() = Position::try_from(8)?;
///
/// assert_eq!(i32::from(record.position()), 8);
/// # Ok::<_, noodles_vcf::record::position::TryFromIntError>(())
/// ```
pub fn position_mut(&mut self) -> &mut vcf::record::Position {
&mut self.pos
}
pub(crate) fn rlen(&self) -> i32 {
self.rlen
}
pub(crate) fn rlen_mut(&mut self) -> &mut i32 {
&mut self.rlen
}
/// Returns the end position of this record.
///
/// This value is 1-based.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert_eq!(record.end().map(i32::from)?, 1);
/// # Ok::<(), io::Error>(())
/// ```
pub fn end(&self) -> io::Result<vcf::record::Position> {
use vcf::record::Position;
let start = i32::from(self.position());
let len = self.rlen();
let end = start + len - 1;
Position::try_from(end).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}
/// Returns the quality score.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert!(record.quality_score().is_none());
/// ```
pub fn quality_score(&self) -> Option<vcf::record::QualityScore> {
self.qual
}
/// Return a mutable reference to the quality score.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// use noodles_vcf::record::QualityScore;
///
/// let mut record = bcf::Record::default();
/// *record.quality_score_mut() = QualityScore::try_from(13.0).map(Some)?;
///
/// assert_eq!(record.quality_score().map(f32::from), Some(13.0));
/// # Ok::<_, noodles_vcf::record::quality_score::TryFromFloatError>(())
/// ```
pub fn quality_score_mut(&mut self) -> &mut Option<vcf::record::QualityScore> {
&mut self.qual
}
/// Returns the IDs.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert!(record.ids().is_empty());
/// ```
pub fn ids(&self) -> &vcf::record::Ids {
&self.id
}
/// Returns a mutable reference to the IDs.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// use noodles_vcf::record::Ids;
///
/// let mut record = bcf::Record::default();
/// let ids: Ids = "nd0".parse()?;
/// *record.ids_mut() = ids.clone();
///
/// assert_eq!(record.ids(), &ids);
/// # Ok::<_, noodles_vcf::record::ids::ParseError>(())
/// ```
pub fn ids_mut(&mut self) -> &mut vcf::record::Ids {
&mut self.id
}
pub(crate) fn reference_bases(&self) -> &vcf::record::ReferenceBases {
&self.r#ref
}
pub(crate) fn alternate_bases(&self) -> &vcf::record::AlternateBases {
&self.alt
}
/// Returns the filters.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert!(record.filters().is_empty());
/// ```
pub fn filters(&self) -> &Filters {
&self.filter
}
pub(crate) fn filters_mut(&mut self) -> &mut Filters {
&mut self.filter
}
/// Returns the info.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert!(record.info().is_empty());
/// ```
pub fn info(&self) -> &Info {
&self.info
}
pub(crate) fn info_mut(&mut self) -> &mut Info {
&mut self.info
}
/// Returns the genotypes.
///
/// # Examples
///
/// ```
/// use noodles_bcf as bcf;
/// let record = bcf::Record::default();
/// assert!(record.genotypes().is_empty());
/// ```
pub fn genotypes(&self) -> &Genotypes {
&self.genotypes
}
pub(crate) fn genotypes_mut(&mut self) -> &mut Genotypes {
&mut self.genotypes
}
}
impl Default for Record {
fn default() -> Self {
use vcf::record::reference_bases::Base;
Self {
chrom: 0,
pos: vcf::record::Position::try_from(1).unwrap(),
rlen: 1,
qual: None,
id: vcf::record::Ids::default(),
r#ref: vcf::record::ReferenceBases::try_from(vec![Base::A]).unwrap(),
alt: vcf::record::AlternateBases::default(),
filter: Filters::default(),
info: Info::default(),
genotypes: Genotypes::default(),
}
}
}