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//! SAM header read group builder.
use std::{collections::HashMap, error, fmt};
use super::{Platform, ReadGroup, Tag};
/// A SAM header reference read group.
#[derive(Debug, Default)]
pub struct Builder {
id: Option<String>,
barcode: Option<String>,
sequencing_center: Option<String>,
description: Option<String>,
produced_at: Option<String>,
flow_order: Option<String>,
key_sequence: Option<String>,
library: Option<String>,
program: Option<String>,
predicted_median_insert_size: Option<i32>,
platform: Option<Platform>,
platform_model: Option<String>,
platform_unit: Option<String>,
sample: Option<String>,
fields: HashMap<Tag, String>,
}
/// An error returned when a SAM header read group fails to build.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum BuildError {
/// The ID is missing.
MissingId,
}
impl error::Error for BuildError {}
impl fmt::Display for BuildError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::MissingId => f.write_str("missing ID"),
}
}
}
impl Builder {
/// Sets a read group ID.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
/// let read_group = ReadGroup::builder().set_id("rg0").build()?;
/// assert_eq!(read_group.id(), "rg0");
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_id<I>(mut self, id: I) -> Self
where
I: Into<String>,
{
self.id = Some(id.into());
self
}
/// Sets a barcode sequence.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_barcode("ACGT")
/// .build()?;
///
/// assert_eq!(read_group.barcode(), Some("ACGT"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_barcode<I>(mut self, barcode: I) -> Self
where
I: Into<String>,
{
self.barcode = Some(barcode.into());
self
}
/// Sets a sequencing center.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_sequencing_center("sc0")
/// .build()?;
///
/// assert_eq!(read_group.sequencing_center(), Some("sc0"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_sequencing_center<I>(mut self, sequencing_center: I) -> Self
where
I: Into<String>,
{
self.sequencing_center = Some(sequencing_center.into());
self
}
/// Sets a description.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_description("noodles")
/// .build()?;
///
/// assert_eq!(read_group.description(), Some("noodles"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_description<I>(mut self, description: I) -> Self
where
I: Into<String>,
{
self.description = Some(description.into());
self
}
/// Sets a datetime of run.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_produced_at("2020-08-19T20:00:00Z")
/// .build()?;
///
/// assert_eq!(read_group.produced_at(), Some("2020-08-19T20:00:00Z"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_produced_at<I>(mut self, produced_at: I) -> Self
where
I: Into<String>,
{
self.produced_at = Some(produced_at.into());
self
}
/// Sets a flow order.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_flow_order("*")
/// .build()?;
///
/// assert_eq!(read_group.flow_order(), Some("*"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_flow_order<I>(mut self, flow_order: I) -> Self
where
I: Into<String>,
{
self.flow_order = Some(flow_order.into());
self
}
/// Sets a key sequence.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_key_sequence("ACGT")
/// .build()?;
///
/// assert_eq!(read_group.key_sequence(), Some("ACGT"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_key_sequence<I>(mut self, key_sequence: I) -> Self
where
I: Into<String>,
{
self.key_sequence = Some(key_sequence.into());
self
}
/// Sets a library.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_library("sample0")
/// .build()?;
///
/// assert_eq!(read_group.library(), Some("sample0"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_library<I>(mut self, library: I) -> Self
where
I: Into<String>,
{
self.library = Some(library.into());
self
}
/// Sets a list of programs used.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_program("noodles")
/// .build()?;
///
/// assert_eq!(read_group.program(), Some("noodles"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_program<I>(mut self, program: I) -> Self
where
I: Into<String>,
{
self.program = Some(program.into());
self
}
/// Sets a predicted median insert size.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_predicted_median_insert_size(101)
/// .build()?;
///
/// assert_eq!(read_group.predicted_median_insert_size(), Some(101));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_predicted_median_insert_size(mut self, predicted_median_insert_size: i32) -> Self {
self.predicted_median_insert_size = Some(predicted_median_insert_size);
self
}
/// Sets a platform.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::{read_group::Platform, ReadGroup};
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_platform(Platform::Illumina)
/// .build()?;
///
/// assert_eq!(read_group.platform(), Some(Platform::Illumina));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_platform(mut self, platform: Platform) -> Self {
self.platform = Some(platform);
self
}
/// Sets a platform model.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_platform_model("noodles")
/// .build()?;
///
/// assert_eq!(read_group.platform_model(), Some("noodles"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_platform_model<I>(mut self, platform_model: I) -> Self
where
I: Into<String>,
{
self.platform_model = Some(platform_model.into());
self
}
/// Sets a platform unit.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_platform_unit("NDLS000.1")
/// .build()?;
///
/// assert_eq!(read_group.platform_unit(), Some("NDLS000.1"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_platform_unit<I>(mut self, platform_unit: I) -> Self
where
I: Into<String>,
{
self.platform_unit = Some(platform_unit.into());
self
}
/// Sets a sample.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .set_sample("sample0")
/// .build()?;
///
/// assert_eq!(read_group.sample(), Some("sample0"));
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn set_sample<I>(mut self, sample: I) -> Self
where
I: Into<String>,
{
self.sample = Some(sample.into());
self
}
/// Inserts a tag-raw value pair.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::{read_group::Tag, ReadGroup};
///
/// let zn = Tag::Other(String::from("zn"));
///
/// let read_group = ReadGroup::builder()
/// .set_id("rg0")
/// .insert(zn.clone(), String::from("noodles"))
/// .build()?;
///
/// assert_eq!(
/// read_group.fields().get(&zn),
/// Some(&String::from("noodles"))
/// );
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn insert<I>(mut self, tag: Tag, value: I) -> Self
where
I: Into<String>,
{
self.fields.insert(tag, value.into());
self
}
/// Builds a reference sequence.
///
/// # Examples
///
/// ```
/// # use noodles_sam::header::read_group::builder;
/// use noodles_sam::header::ReadGroup;
/// let read_group = ReadGroup::builder().set_id("rg0").build()?;
/// # Ok::<(), builder::BuildError>(())
/// ```
pub fn build(self) -> Result<ReadGroup, BuildError> {
let id = self.id.ok_or(BuildError::MissingId)?;
Ok(ReadGroup {
id,
barcode: self.barcode,
sequencing_center: self.sequencing_center,
description: self.description,
produced_at: self.produced_at,
flow_order: self.flow_order,
key_sequence: self.key_sequence,
library: self.library,
program: self.program,
predicted_median_insert_size: self.predicted_median_insert_size,
platform: self.platform,
platform_model: self.platform_model,
platform_unit: self.platform_unit,
sample: self.sample,
fields: self.fields,
})
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_build() {
assert_eq!(Builder::default().build(), Err(BuildError::MissingId));
}
}