Struct RecordBuf

pub struct RecordBuf { /* private fields */ }

An alignment record buffer.

Implementations

impl RecordBuf

pub fn try_from_alignment_record<R>(header: &Header, record: &R) -> Result<Self>

where R: Record,

Converts an alignment record to a buffer.

Examples

use noodles_sam::{self as sam, alignment::RecordBuf};

let header = sam::Header::default();
let record = sam::Record::default();

let record_buf = RecordBuf::try_from_alignment_record(&header, &record)?;

assert_eq!(record_buf, RecordBuf::default());

impl RecordBuf

pub fn builder() -> Builder

Creates an alignment record builder.

Examples

use noodles_sam as sam;
let builder = sam::alignment::RecordBuf::builder();

pub fn name(&self) -> Option<&BStr>

Returns the name.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.name().is_none());

pub fn name_mut(&mut self) -> &mut Option<BString>

Returns a mutable reference to the name.

Examples

use bstr::ByteSlice;
use noodles_sam as sam;

let mut record = sam::alignment::RecordBuf::default();
*record.name_mut() = Some("r1".into());

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

pub fn flags(&self) -> Flags

Returns the flags.

Examples

use noodles_sam::{self as sam, alignment::record::Flags};
let record = sam::alignment::RecordBuf::default();
assert_eq!(record.flags(), Flags::UNMAPPED);

pub fn flags_mut(&mut self) -> &mut Flags

Returns a mutable reference to the flags.

Examples

use noodles_sam::{self as sam, alignment::record::Flags};
let mut record = sam::alignment::RecordBuf::default();
*record.flags_mut() = Flags::empty();
assert!(record.flags().is_empty());

pub fn reference_sequence_id(&self) -> Option<usize>

Returns the reference sequence ID.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.reference_sequence_id().is_none());

pub fn reference_sequence_id_mut(&mut self) -> &mut Option<usize>

Returns a mutable reference to the reference sequence ID.

Examples

use noodles_sam as sam;
let mut record = sam::alignment::RecordBuf::default();
*record.reference_sequence_id_mut() = Some(0);
assert_eq!(record.reference_sequence_id(), Some(0));

pub fn alignment_start(&self) -> Option<Position>

Returns the alignment start.

This position is 1-based, inclusive.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.alignment_start().is_none());

pub fn alignment_start_mut(&mut self) -> &mut Option<Position>

Returns a mutable reference to the alignment start.

This position is 1-based, inclusive.

Examples

use noodles_core::Position;
use noodles_sam as sam;
let mut record = sam::alignment::RecordBuf::default();
*record.alignment_start_mut() = Some(Position::MIN);
assert_eq!(record.alignment_start(), Some(Position::MIN));

pub fn mapping_quality(&self) -> Option<MappingQuality>

Returns the mapping quality.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.mapping_quality().is_none());

pub fn mapping_quality_mut(&mut self) -> &mut Option<MappingQuality>

Returns a mutable reference to the mapping quality.

Examples

use noodles_sam::{self as sam, alignment::record::MappingQuality};
let mut record = sam::alignment::RecordBuf::default();
*record.mapping_quality_mut() = Some(MappingQuality::MIN);
assert_eq!(record.mapping_quality(), Some(MappingQuality::MIN));

pub fn cigar(&self) -> &Cigar

Returns the CIGAR operations.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.cigar().as_ref().is_empty());

pub fn cigar_mut(&mut self) -> &mut Cigar

Returns a mutable reference to 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 mut record = sam::alignment::RecordBuf::default();
*record.cigar_mut() = cigar.clone();

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

pub fn mate_reference_sequence_id(&self) -> Option<usize>

Returns the mate reference sequence ID.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.mate_reference_sequence_id().is_none());

pub fn mate_reference_sequence_id_mut(&mut self) -> &mut Option<usize>

Returns a mutable reference to the mate reference sequence ID.

Examples

use noodles_sam as sam;
let mut record = sam::alignment::RecordBuf::default();
*record.mate_reference_sequence_id_mut() = Some(0);
assert_eq!(record.mate_reference_sequence_id(), Some(0));

pub fn mate_alignment_start(&self) -> Option<Position>

Returns the mate alignment start.

This position is 1-based, inclusive.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.mate_alignment_start().is_none());

pub fn mate_alignment_start_mut(&mut self) -> &mut Option<Position>

Returns a mutable reference to the mate alignment start.

This position is 1-based, inclusive.

Examples

use noodles_core::Position;
use noodles_sam as sam;
let mut record = sam::alignment::RecordBuf::default();
*record.mate_alignment_start_mut() = Some(Position::MIN);
assert_eq!(record.mate_alignment_start(), Some(Position::MIN));

pub fn template_length(&self) -> i32

Returns the template length.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert_eq!(record.template_length(), 0);

pub fn template_length_mut(&mut self) -> &mut i32

Returns a mutable reference to template length.

Examples

use noodles_sam as sam;
let mut record = sam::alignment::RecordBuf::default();
*record.template_length_mut() = 4;
assert_eq!(record.template_length(), 4);

pub fn sequence(&self) -> &Sequence

Returns the sequence.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.sequence().is_empty());

pub fn sequence_mut(&mut self) -> &mut Sequence

Returns a mutable reference to sequence.

Examples

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

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

let mut record = sam::alignment::RecordBuf::default();
*record.sequence_mut() = sequence.clone();

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

pub fn quality_scores(&self) -> &QualityScores

Returns the quality scores.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.quality_scores().is_empty());

pub fn quality_scores_mut(&mut self) -> &mut QualityScores

Returns a mutable reference to quality scores.

Examples

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

let quality_scores = QualityScores::default();

let mut record = sam::alignment::RecordBuf::default();
*record.quality_scores_mut() = quality_scores.clone();

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

pub fn data(&self) -> &Data

Returns the data.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.data().is_empty());

pub fn data_mut(&mut self) -> &mut Data

Returns a mutable reference to 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 mut record = sam::alignment::RecordBuf::default();
*record.data_mut() = data.clone();

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

pub fn reference_sequence<'a>( &self, header: &'a Header, ) -> Option<Result<(&'a [u8], &'a Map<ReferenceSequence>)>>

Returns the associated reference sequence.

Examples

use noodles_sam as sam;
let header = sam::Header::default();
let record = sam::alignment::RecordBuf::default();
assert!(record.reference_sequence(&header).is_none());

pub fn mate_reference_sequence<'a>( &self, header: &'a Header, ) -> Option<Result<(&'a [u8], &'a Map<ReferenceSequence>)>>

Returns the associated mate reference sequence.

Examples

use noodles_sam as sam;
let header = sam::Header::default();
let record = sam::alignment::RecordBuf::default();
assert!(record.mate_reference_sequence(&header).is_none());

pub fn alignment_span(&self) -> Option<usize>

Returns the alignment span.

Examples

use noodles_sam as sam;
let record = sam::alignment::RecordBuf::default();
assert!(record.alignment_span().is_none());

pub fn alignment_end(&self) -> Option<Position>

Calculates the end position.

Examples

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

let record = sam::alignment::RecordBuf::builder()
    .set_alignment_start(Position::try_from(8)?)
    .set_cigar([Op::new(Kind::Match, 5)].into_iter().collect())
    .build();

assert_eq!(record.alignment_end(), Position::new(12));

Trait Implementations

impl Clone for RecordBuf

fn clone(&self) -> RecordBuf

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for RecordBuf

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

Formats the value using the given formatter.

impl Default for RecordBuf

fn default() -> Self

Returns the “default value” for a type.

impl PartialEq for RecordBuf

fn eq(&self, other: &RecordBuf) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Record for RecordBuf

fn name(&self) -> Option<&BStr>

Returns the name.

fn flags(&self) -> Result<Flags>

Returns the flags.

fn reference_sequence_id<'r, 'h: 'r>( &'r self, _: &'h Header, ) -> Option<Result<usize>>

Returns the reference sequence ID.

fn alignment_start(&self) -> Option<Result<Position>>

Returns the alignment start.

fn mapping_quality(&self) -> Option<Result<MappingQuality>>

Returns the mapping quality.

fn cigar(&self) -> Box<dyn Cigar + '_>

Returns the CIGAR operations.

fn mate_reference_sequence_id<'r, 'h: 'r>( &'r self, _: &'h Header, ) -> Option<Result<usize>>

Returns the mate reference sequence ID.

fn mate_alignment_start(&self) -> Option<Result<Position>>

Returns the mate alignment start.

fn template_length(&self) -> Result<i32>

Returns the template length.

fn sequence(&self) -> Box<dyn Sequence + '_>

Returns the sequence.

fn quality_scores(&self) -> Box<dyn QualityScores + '_>

Returns the quality scores.

fn data(&self) -> Box<dyn Data + '_>

Returns the data.

fn reference_sequence<'h>( &self, header: &'h Header, ) -> Option<Result<(&'h BStr, &'h Map<ReferenceSequence>)>>

Returns the associated reference sequence.

fn mate_reference_sequence<'h>( &self, header: &'h Header, ) -> Option<Result<(&'h BStr, &'h Map<ReferenceSequence>)>>

Returns the associated mate reference sequence.

fn alignment_span(&self) -> Option<Result<usize>>

Returns the alignment span.

fn alignment_end(&self) -> Option<Result<Position>>

Calculates the end position.

impl StructuralPartialEq for RecordBuf