noodles_sam::alignment::record

Trait Record

pub trait Record {
Show 16 methods    // Required methods
    fn name(&self) -> Option<&BStr>;
    fn flags(&self) -> Result<Flags>;
    fn reference_sequence_id<'r, 'h: 'r>(
        &'r self,
        header: &'h Header,
    ) -> Option<Result<usize>>;
    fn alignment_start(&self) -> Option<Result<Position>>;
    fn mapping_quality(&self) -> Option<Result<MappingQuality>>;
    fn cigar(&self) -> Box<dyn Cigar + '_>;
    fn mate_reference_sequence_id<'r, 'h: 'r>(
        &'r self,
        header: &'h Header,
    ) -> Option<Result<usize>>;
    fn mate_alignment_start(&self) -> Option<Result<Position>>;
    fn template_length(&self) -> Result<i32>;
    fn sequence(&self) -> Box<dyn Sequence + '_>;
    fn quality_scores(&self) -> Box<dyn QualityScores + '_>;
    fn data(&self) -> Box<dyn Data + '_>;

    // Provided methods
    fn reference_sequence<'h>(
        &self,
        header: &'h Header,
    ) -> Option<Result<(&'h BStr, &'h Map<ReferenceSequence>)>> { ... }
    fn mate_reference_sequence<'h>(
        &self,
        header: &'h Header,
    ) -> Option<Result<(&'h BStr, &'h Map<ReferenceSequence>)>> { ... }
    fn alignment_span(&self) -> Option<Result<usize>> { ... }
    fn alignment_end(&self) -> Option<Result<Position>> { ... }
}

Expand description

An alignment record.

Required Methods§

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.

This position is 1-based, inclusive.

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.

This position is 1-based, inclusive.

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.

Provided Methods§

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.

This position is 1-based, inclusive.

Trait Implementations§

impl Record for Box<dyn 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. Read more

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. Read more

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. Read more

Implementations on Foreign Types§

impl Record for Box<dyn Record>

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

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

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

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

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

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

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

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

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

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

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

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

Implementors§

impl Record for Record

impl Record for RecordBuf