Struct Record

pub struct Record(/* private fields */);

A SAM record.

Implementations

impl Record

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

Returns the name.

Examples

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

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

Returns the flags.

Examples

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

pub fn reference_sequence_id(&self, header: &Header) -> Option<Result<usize>>

Returns the reference sequence ID.

Examples

use noodles_sam as sam;
let header = sam::Header::default();
let record = sam::Record::default();
assert!(record.reference_sequence_id(&header).is_none());

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

Returns the reference sequence name.

Examples

use noodles_sam as sam;
let record = sam::Record::default();
assert!(record.reference_sequence_name().is_none());

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

Returns the alignment start.

This position is 1-based, inclusive.

Examples

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

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

Returns the mapping quality.

Examples

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

pub fn cigar(&self) -> Cigar<'_>

Returns the CIGAR operations.

Examples

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

pub fn mate_reference_sequence_id( &self, header: &Header, ) -> Option<Result<usize>>

Returns the mate reference sequence ID.

Examples

use noodles_sam as sam;
let header = sam::Header::default();
let record = sam::Record::default();
assert!(record.mate_reference_sequence_id(&header).is_none());

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

Returns the mate reference sequence name.

Examples

use noodles_sam as sam;
let record = sam::Record::default();
assert!(record.mate_reference_sequence_name().is_none());

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

Returns the mate alignment start.

This position is 1-based, inclusive.

Examples

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

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

Returns the template length.

Examples

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

pub fn sequence(&self) -> Sequence<'_>

Returns the sequence.

Examples

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

pub fn quality_scores(&self) -> QualityScores<'_>

Returns the quality scores.

Examples

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

pub fn data(&self) -> Data<'_>

Returns the data.

Examples

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

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

fn default() -> Record

Returns the “default value” for a type.

impl PartialEq for Record

fn eq(&self, other: &Record) -> 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 Record

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, header: &'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, header: &'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 TryFrom<&[u8]> for Record

type Error = Error

The type returned in the event of a conversion error.

fn try_from(buf: &[u8]) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for Record

impl StructuralPartialEq for Record