Struct Builder

pub struct Builder { /* private fields */ }

An alignment record builder.

Implementations

impl Builder

pub fn set_name<N>(self, name: N) -> Self

where N: Into<BString>,

Sets the read name.

Examples

use bstr::ByteSlice;
use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_name("r1")
    .build();

assert_eq!(record.name(), Some(b"r1".as_bstr()));

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

Sets the flags.

Examples

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

let record = sam::alignment::RecordBuf::builder()
    .set_flags(Flags::empty())
    .build();

assert_eq!(record.flags(), Flags::empty());

pub fn set_reference_sequence_id(self, reference_sequence_id: usize) -> Self

Sets the reference sequence ID.

Examples

use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_reference_sequence_id(0)
    .build();

assert_eq!(record.reference_sequence_id(), Some(0));

pub fn set_alignment_start(self, alignment_start: Position) -> Self

Sets the alignment start.

Examples

use noodles_core::Position;
use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_alignment_start(Position::MIN)
    .build();

assert_eq!(record.alignment_start(), Some(Position::MIN));

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

Sets the mapping quality.

Examples

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

let record = sam::alignment::RecordBuf::builder()
    .set_mapping_quality(MappingQuality::MIN)
    .build();

assert_eq!(record.mapping_quality(), Some(MappingQuality::MIN));

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

Sets the CIGAR operations.

Examples

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

let cigar: Cigar = [Op::new(Kind::Match, 4)].into_iter().collect();

let record = sam::alignment::RecordBuf::builder()
    .set_cigar(cigar.clone())
    .build();

assert_eq!(record.cigar(), &cigar);

pub fn set_mate_reference_sequence_id( self, mate_reference_sequence_id: usize, ) -> Self

Sets the mate reference sequence ID.

Examples

use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_mate_reference_sequence_id(0)
    .build();

assert_eq!(record.mate_reference_sequence_id(), Some(0));

pub fn set_mate_alignment_start(self, mate_alignment_start: Position) -> Self

Sets the mate alignment start.

Examples

use noodles_core::Position;
use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_mate_alignment_start(Position::MIN)
    .build();

assert_eq!(record.mate_alignment_start(), Some(Position::MIN));

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

Sets the template length.

Examples

use noodles_sam as sam;

let record = sam::alignment::RecordBuf::builder()
    .set_template_length(4)
    .build();

assert_eq!(record.template_length(), 4);

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

Sets the sequence.

Examples

use noodles_sam::{self as sam, alignment::record_buf::Sequence};

let sequence = Sequence::from(b"ACGT");

let record = sam::alignment::RecordBuf::builder()
    .set_sequence(sequence.clone())
    .build();

assert_eq!(record.sequence(), &sequence);

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

Sets the quality scores.

Examples

use noodles_sam::{self as sam, alignment::record_buf::QualityScores};

let quality_scores = QualityScores::from(vec![45, 35, 43, 50]);

let record = sam::alignment::RecordBuf::builder()
    .set_quality_scores(quality_scores.clone())
    .build();

assert_eq!(record.quality_scores(), &quality_scores);

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

Sets the data.

Examples

use noodles_sam::{
    self as sam,
    alignment::{
        record::data::field::Tag,
        record_buf::{data::field::Value, Data},
    },
};

let data: Data = [(Tag::ALIGNMENT_HIT_COUNT, Value::from(1))]
    .into_iter()
    .collect();

let record = sam::alignment::RecordBuf::builder()
    .set_data(data.clone())
    .build();

assert_eq!(record.data(), &data);

pub fn build(self) -> RecordBuf

Builds the alignment record.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::builder().build();
assert_eq!(record, sam::alignment::RecordBuf::default());

Trait Implementations

impl Debug for Builder

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

Formats the value using the given formatter.

impl Default for Builder

fn default() -> Self

Returns the “default value” for a type.