Struct noodles::cram::Record

pub struct Record { /* private fields */ }

A CRAM record.

Implementations

impl Record

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

where R: Record + ?Sized,

Converts an alignment record to a CRAM record.

pub fn try_into_alignment_record( self, header: &Header ) -> Result<RecordBuf, Error>

Converts this CRAM record to an alignment record.

impl Record

pub fn builder() -> Builder

Returns a builder to create a record from each of its fields.

pub fn bam_flags(&self) -> Flags

Returns the BAM flags.

This is also called the BAM bit flags.

pub fn flags(&self) -> Flags

Returns the SAM flags.

pub fn cram_flags(&self) -> Flags

Returns the CRAM flags.

This is also called the CRAM bit flags or compression bit flags.

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

Returns the reference sequence ID.

This is also called the reference ID. It is the position of the reference sequence in the SAM header.

pub fn reference_sequence<'h>( &self, reference_sequences: &'h IndexMap<BString, Map<ReferenceSequence>> ) -> Option<Result<(&'h [u8], &'h Map<ReferenceSequence>), Error>>

Returns the associated reference sequence.

pub fn read_length(&self) -> usize

Returns the read length.

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

Returns the alignment start.

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

Returns the alignment end.

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

Returns the read group ID.

This is also simply called the read group. It is the position of the read group in the SAM header.

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

Returns the name.

pub fn next_mate_flags(&self) -> NextMateFlags

Returns the next mate flags.

This is also call the next mate bit flags.

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

Returns the reference sequence ID of the next fragment.

It is the position of the reference sequence in the SAM header.

pub fn mate_reference_sequence<'h>( &self, reference_sequences: &'h IndexMap<BString, Map<ReferenceSequence>> ) -> Option<Result<(&'h [u8], &'h Map<ReferenceSequence>), Error>>

Returns the associated mate reference sequence.

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

Returns the alignment start position of the next mate.

This value is 1-based.

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

Returns the alignment start.

pub fn template_size(&self) -> i32

Returns the template size.

pub fn template_length(&self) -> i32

Returns the template size.

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

Returns the distance to the next fragment.

This is the number of records to the next fragment within a slice.

pub fn tags(&self) -> &Data

Returns the tag dictionary.

pub fn data(&self) -> &Data

Returns the data.

pub fn bases(&self) -> &Sequence

Returns the read bases.

pub fn sequence(&self) -> &Sequence

Returns the sequence.

pub fn features(&self) -> &Features

Returns the read features.

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

Returns the mapping quality.

pub fn quality_scores(&self) -> &QualityScores

Returns the quality scores.

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<(), Error>

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

This method tests for self and other values to be equal, and is used by ==.

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

This method 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<Box<dyn Name + '_>>

Returns the name.

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

Returns the flags.

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

where 'h: 'r,

Returns the reference sequence ID.

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

Returns the alignment start.

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

Returns the mapping quality.

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

Returns the CIGAR operations.

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

where 'h: 'r,

Returns the mate reference sequence ID.

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

Returns the mate alignment start.

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

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>), Error>>

Returns the associated reference sequence.

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

Returns the associated mate reference sequence.

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

Returns the alignment span.

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

Calculates the end position.

impl StructuralPartialEq for Record