Struct noodles::sam::header::ReadGroup[−][src]

pub struct ReadGroup { /* fields omitted */ }

Expand description

A SAM header read group.

A read group typically defines the set of reads that came from the same run on a sequencing instrument. The read group ID is guaranteed to be set.

Implementations

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impl ReadGroup

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pub fn builder() -> Builder

Creates a SAM header read group builder.

Examples

use noodles_sam::header::ReadGroup;
let builder = ReadGroup::builder();

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pub fn new(id: I) -> ReadGroup where
I: Into<String>,

Creates a read group with an ID.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert_eq!(read_group.id(), "rg0");

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pub fn id(&self) -> &str

Returns the read group ID.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert_eq!(read_group.id(), "rg0");

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pub fn id_mut(&mut self) -> &mut String

Returns a mutable reference to the read group ID.

Examples

use noodles_sam::header::ReadGroup;

let mut read_group = ReadGroup::new("rg0");
assert_eq!(read_group.id(), "rg0");

*read_group.id_mut() = String::from("rg1");
assert_eq!(read_group.id(), "rg1");

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pub fn barcode(&self) -> Option<&str>

Returns the barcode sequence.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.barcode().is_none());

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pub fn sequencing_center(&self) -> Option<&str>

Returns the sequencing center.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.sequencing_center().is_none());

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pub fn description(&self) -> Option<&str>

Returns the description.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.description().is_none());

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pub fn produced_at(&self) -> Option<&str>

Returns the datatime of run.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.produced_at().is_none());

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pub fn flow_order(&self) -> Option<&str>

Returns the flow order.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.flow_order().is_none());

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pub fn key_sequence(&self) -> Option<&str>

Returns the key sequence.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.key_sequence().is_none());

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pub fn library(&self) -> Option<&str>

Returns the library.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.library().is_none());

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pub fn program(&self) -> Option<&str>

Returns the programs used.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.program().is_none());

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pub fn predicted_median_insert_size(&self) -> Option<i32>

Returns the predicted median insert size.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.predicted_median_insert_size().is_none());

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pub fn platform(&self) -> Option<Platform>

Returns the platform used.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.platform().is_none());

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pub fn platform_model(&self) -> Option<&str>

Returns the platform model.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.platform_model().is_none());

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pub fn platform_unit(&self) -> Option<&str>

Returns the platform unit.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.platform_unit().is_none());

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pub fn sample(&self) -> Option<&str>

Returns the sample.

Examples

use noodles_sam::header::ReadGroup;
let read_group = ReadGroup::new("rg0");
assert!(read_group.sample().is_none());

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pub fn fields(&self) -> &HashMap<Tag, String, RandomState>

Returns the raw fields of the read group.

This includes any field that is not specially handled by the structure itself. For example, this will not include the ID field, as it is parsed and available as Self::id.

Examples

use noodles_sam::header::{read_group::Tag, ReadGroup};

let read_group = ReadGroup::builder()
    .set_id("rg0")
    .insert(Tag::Other(String::from("zn")), String::from("noodles"))
    .build()?;

let fields = read_group.fields();
assert_eq!(fields.len(), 1);
assert_eq!(
    fields.get(&Tag::Other(String::from("zn"))),
    Some(&String::from("noodles"))
);

assert_eq!(fields.get(&Tag::Id), None);
assert_eq!(read_group.id(), "rg0");