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bcf/record/samples: Remove Samples::try_into_vcf_record_samples
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@zaeleus
zaeleus committed Mar 21, 2024
1 parent 1b1eb39 commit 02135fc
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Showing 3 changed files with 93 additions and 48 deletions.
52 changes: 46 additions & 6 deletions noodles-bcf/src/async/io/reader/record.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,20 @@ mod tests {
variant::{
record::{
info::{self, field::Value as InfoFieldValue},
samples, AlternateBases, Filters, Info,
samples::{self, Sample},
AlternateBases, Filters, Info, Samples,
},
record_buf::{
samples::{sample::Value as GenotypeFieldValue, Keys},
samples::{
sample::{
value::{
genotype::{allele::Phasing, Allele},
Genotype,
},
Value as GenotypeFieldValue,
},
Keys,
},
Samples as VcfGenotypes,
},
},
Expand Down Expand Up @@ -116,7 +126,28 @@ mod tests {

// genotypes

let actual = record.samples()?.try_into_vcf_record_samples(&header)?;
let samples = record.samples()?;

let column_names: Vec<_> = samples
.column_names(&header)
.map(|result| result.map(String::from))
.collect::<io::Result<_>>()?;
let keys = Keys::try_from(column_names)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;

let values = samples
.iter()
.map(|sample| {
sample
.iter(&header)
.map(|result| {
result.and_then(|(_, value)| value.map(|v| v.try_into()).transpose())
})
.collect()
})
.collect::<io::Result<_>>()?;

let actual = VcfGenotypes::new(keys, values);

let expected = VcfGenotypes::new(
Keys::try_from(vec![
Expand All @@ -128,21 +159,30 @@ mod tests {
])?,
vec![
vec![
Some(GenotypeFieldValue::from("0/0")),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(0), Phasing::Unphased),
Allele::new(Some(0), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::from(10)),
Some(GenotypeFieldValue::from(32)),
Some(GenotypeFieldValue::from(vec![Some(32), Some(0)])),
Some(GenotypeFieldValue::from(vec![Some(0), Some(10), Some(100)])),
],
vec![
Some(GenotypeFieldValue::from("0/1")),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(0), Phasing::Unphased),
Allele::new(Some(1), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::from(10)),
Some(GenotypeFieldValue::from(48)),
Some(GenotypeFieldValue::from(vec![Some(32), Some(16)])),
Some(GenotypeFieldValue::from(vec![Some(10), Some(0), Some(100)])),
],
vec![
Some(GenotypeFieldValue::from("1/1")),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(1), Phasing::Unphased),
Allele::new(Some(1), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::from(10)),
Some(GenotypeFieldValue::from(64)),
Some(GenotypeFieldValue::from(vec![Some(0), Some(64)])),
Expand Down
52 changes: 46 additions & 6 deletions noodles-bcf/src/io/reader/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -108,11 +108,21 @@ pub(crate) mod tests {
use noodles_vcf::{
self as vcf,
variant::{
record::{info, samples, AlternateBases, Filters, Info},
record::{
info,
samples::{self, Sample},
AlternateBases, Filters, Info, Samples,
},
record_buf::{
info::field::Value as InfoFieldValue,
samples::{
sample::{value::Array, Value as GenotypeFieldValue},
sample::{
value::{
genotype::{allele::Phasing, Allele},
Array, Genotype,
},
Value as GenotypeFieldValue,
},
Keys,
},
Samples as VcfGenotypes,
Expand Down Expand Up @@ -186,7 +196,28 @@ pub(crate) mod tests {

// genotypes

let actual = record.samples()?.try_into_vcf_record_samples(&header)?;
let samples = record.samples()?;

let column_names: Vec<_> = samples
.column_names(&header)
.map(|result| result.map(String::from))
.collect::<io::Result<_>>()?;
let keys = Keys::try_from(column_names)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;

let values = samples
.iter()
.map(|sample| {
sample
.iter(&header)
.map(|result| {
result.and_then(|(_, value)| value.map(|v| v.try_into()).transpose())
})
.collect()
})
.collect::<io::Result<_>>()?;

let actual = VcfGenotypes::new(keys, values);

let expected = VcfGenotypes::new(
Keys::try_from(vec![
Expand All @@ -198,7 +229,10 @@ pub(crate) mod tests {
])?,
vec![
vec![
Some(GenotypeFieldValue::String(String::from("0/0"))),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(0), Phasing::Unphased),
Allele::new(Some(0), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::Integer(10)),
Some(GenotypeFieldValue::Integer(32)),
Some(GenotypeFieldValue::Array(Array::Integer(vec![
Expand All @@ -212,7 +246,10 @@ pub(crate) mod tests {
]))),
],
vec![
Some(GenotypeFieldValue::String(String::from("0/1"))),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(0), Phasing::Unphased),
Allele::new(Some(1), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::Integer(10)),
Some(GenotypeFieldValue::Integer(48)),
Some(GenotypeFieldValue::Array(Array::Integer(vec![
Expand All @@ -226,7 +263,10 @@ pub(crate) mod tests {
]))),
],
vec![
Some(GenotypeFieldValue::String(String::from("1/1"))),
Some(GenotypeFieldValue::Genotype(Genotype::try_from(vec![
Allele::new(Some(1), Phasing::Unphased),
Allele::new(Some(1), Phasing::Unphased),
])?)),
Some(GenotypeFieldValue::Integer(10)),
Some(GenotypeFieldValue::Integer(64)),
Some(GenotypeFieldValue::Array(Array::Integer(vec![
Expand Down
37 changes: 1 addition & 36 deletions noodles-bcf/src/record/samples.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ pub mod series;

use std::{io, iter};

use noodles_vcf::{self as vcf, variant::record::Samples as _};
use noodles_vcf as vcf;

use self::series::read_series;
pub use self::{sample::Sample, series::Series};
Expand All @@ -27,41 +27,6 @@ impl<'r> Samples<'r> {
}
}

/// Converts BCF record samples to VCF record samples.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_bcf::record::Samples;
/// use noodles_vcf as vcf;
///
/// let bcf_samples = Samples::default();
///
/// let header = vcf::Header::default();
/// let vcf_samples = bcf_samples.try_into_vcf_record_samples(&header)?;
///
/// assert!(vcf_samples.is_empty());
/// # Ok::<_, io::Error>(())
/// ```
pub fn try_into_vcf_record_samples(
&self,
header: &vcf::Header,
) -> io::Result<vcf::variant::record_buf::Samples> {
use crate::record::codec::decoder::read_samples;

if self.is_empty() {
return Ok(vcf::variant::record_buf::Samples::default());
}

let mut reader = self.src;

let genotypes = read_samples(&mut reader, header, self.len(), self.format_count())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;

Ok(genotypes)
}

/// Returns the number of fields per sample.
///
/// # Examples
Expand Down

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