Struct noodles::sam::record::Builder

pub struct Builder { /* fields omitted */ }

A SAM record builder.

Implementations

impl Builder

pub fn new() -> Builder

Creates a SAM record builder.

Typically, Record::builder is used instead of calling this.

Examples

use noodles_sam as sam;
let builder = sam::Record::builder();

pub fn set_read_name(self, read_name: ReadName) -> Builder

Sets a SAM record read name.

Examples

use noodles_sam as sam;

let record = sam::Record::builder()
    .set_read_name("r0".parse()?)
    .build()?;

assert_eq!(record.read_name().map(|name| name.as_str()), Some("r0"));
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_flags(self, flags: Flags) -> Builder

Sets SAM record flags.

Examples

use noodles_sam::{self as sam, record::Flags};

let record = sam::Record::builder()
    .set_flags(Flags::PAIRED | Flags::READ_1)
    .build()?;

assert_eq!(record.flags(), Flags::PAIRED | Flags::READ_1);

pub fn set_reference_sequence_name(
    self,
    reference_sequence_name: ReferenceSequenceName
) -> Builder

Sets a SAM record reference sequence name.

Examples

use noodles_sam as sam;

let record = sam::Record::builder()
    .set_reference_sequence_name("sq0".parse()?)
    .build()?;

assert_eq!(record.reference_sequence_name().map(|name| name.as_str()), Some("sq0"));
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_position(self, position: Position) -> Builder

Sets a SAM record position.

This value is 1-based.

Examples

use noodles_sam::{self as sam, record::Position};

let record = sam::Record::builder()
    .set_position(Position::try_from(13)?)
    .build()?;

assert_eq!(record.position().map(i32::from), Some(13));

pub fn set_mapping_quality(self, mapping_quality: MappingQuality) -> Builder

Sets a SAM record mapping quality.

Examples

use noodles_sam::{self as sam, record::MappingQuality};

let record = sam::Record::builder()
    .set_mapping_quality(MappingQuality::from(34))
    .build()?;

assert_eq!(*record.mapping_quality(), Some(34));

pub fn set_cigar(self, cigar: Cigar) -> Builder

Sets a SAM record CIGAR.

Examples

use noodles_sam::{self as sam, record::cigar::{op::Kind, Op}};

let record = sam::Record::builder()
    .set_cigar("36M".parse()?)
    .build()?;

assert_eq!(**record.cigar(), [Op::new(Kind::Match, 36)]);
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_mate_reference_sequence_name(
    self,
    mate_reference_sequence_name: ReferenceSequenceName
) -> Builder

Sets a SAM record mate reference sequence name.

This value is 1-based.

Examples

use noodles_sam as sam;

let record = sam::Record::builder()
    .set_mate_reference_sequence_name("sq0".parse()?)
    .build()?;

assert_eq!(record.mate_reference_sequence_name().map(|name| name.as_str()), Some("sq0"));
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_mate_position(self, mate_position: Position) -> Builder

Sets a SAM record mate position.

Examples

use noodles_sam::{self as sam, record::Position};

let record = sam::Record::builder()
    .set_mate_position(Position::try_from(17)?)
    .build()?;

assert_eq!(record.mate_position().map(i32::from), Some(17));

pub fn set_template_length(self, template_length: i32) -> Builder

Sets a SAM record template length.

Examples

use noodles_sam as sam;
let record = sam::Record::builder().set_template_length(36).build()?;
assert_eq!(record.template_length(), 36);

pub fn set_sequence(self, sequence: Sequence) -> Builder

Sets a SAM record sequence.

Examples

use noodles_sam::{self as sam, record::sequence::Base};

let record = sam::Record::builder()
    .set_cigar("4M".parse()?)
    .set_sequence("ACGT".parse()?)
    .set_quality_scores("NDLS".parse()?)
    .build()?;

assert_eq!(**record.sequence(), [Base::A, Base::C, Base::G, Base::T]);
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_quality_scores(self, quality_scores: QualityScores) -> Builder

Sets SAM record quality scores.

Examples

use noodles_sam::{self as sam, record::quality_scores::Score};

let record = sam::Record::builder()
    .set_cigar("2M".parse()?)
    .set_sequence("AC".parse()?)
    .set_quality_scores("ND".parse()?)
    .build()?;

assert_eq!(**record.quality_scores(), [
    Score::try_from('N')?,
    Score::try_from('D')?,
]);
Ok::<(), Box<dyn std::error::Error>>(())

pub fn set_data(self, data: Data) -> Builder

Sets SAM record data.

Examples

use noodles_sam::{self as sam, record::{data, Data}};

let record = sam::Record::default();
assert!(record.data().is_empty());

let data = Data::try_from(vec![data::Field::new(
    data::field::Tag::AlignmentHitCount,
    data::field::Value::Int(1),
)])?;
let record = sam::Record::builder().set_data(data).build()?;
assert_eq!(record.data().to_string(), "NH:i:1");

pub fn build(self) -> Result<Record, BuildError>

Builds a SAM record.

Example

use noodles_sam as sam;
let record = sam::Record::builder().build()?;

Trait Implementations

impl Debug for Builder

pub fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl Default for Builder

pub fn default() -> Builder

Returns the “default value” for a type.