Struct bam::pileup::PileupEntry

pub struct PileupEntry { /* fields omitted */ }

Single record that covers a reference position. Part of a pileup column.

Implementations

impl PileupEntry

pub fn record(&self) -> &Rc<Record>

Returns a smart pointer to the record.

pub fn query_start(&self) -> u32

Returns 0-based index of the first base aligned to the reference position. If the position is deleted in the record, the function returns the index of the last aligned base before the reference position.

pub fn query_end(&self) -> u32

Returns 0-based index after the last base aligned to the reference position. If the position is deleted in the record, the function returns the index of the last aligned base before the reference position. In that case query_start is the same as query_end.

pub fn len(&self) -> u32

Returns the size of the record sequence aligned to the reference position. (same as query_end() - query_start()).

pub fn aln_type(&self) -> AlnType

Returns the type of the region aligned to the reference position (deletion, match or insertion).

pub fn ref_pos(&self) -> u32

Returns the current reference position.

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

Returns an iterator over nucleotides in the region aligned to the reference position, if the sequence is present in the record.

pub fn qualities(&self) -> Option<&[u8]>

Returns raw qualities (without +33) in the region aligned to the reference position, if the qualities are present in the record.

pub fn is_aln_start(&self) -> bool

Returns true if the record alignment starts at the reference position.

pub fn is_aln_end(&self) -> bool

Returns true if the record alignment ends at the reference position (it is the last aligned position).

pub fn cigar_index(&self) -> usize

Returns the current CIGAR index.

pub fn cigar_remaining(&self) -> u32

Returns the remaining length of the current CIGAR operation. The remaining length includes the current position.

Trait Implementations

impl Clone for PileupEntry

fn clone(&self) -> PileupEntry

Returns a copy of the value.

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

Performs copy-assignment from source.