Struct rust_htslib::bam::buffer::RecordBuffer

pub struct RecordBuffer { /* fields omitted */ }

A buffer for BAM records. This allows access regions in a sorted BAM file while iterating over it in a single pass. The buffer is implemented as a ringbuffer, such that extension or movement to the right has linear complexity. The buffer makes use of indexed random access. Hence, when fetching a region at the very end of the BAM, everything before is omitted without cost.

Methods

impl RecordBuffer

pub fn new(bam: IndexedReader, cache_cigar: bool) -> Self

Create a new RecordBuffer.

Arguments

• bam - BAM reader
• cache_cigar - whether to call bam::Record::cache_cigar() for each record.

pub fn fetch(
    &mut self,
    chrom: &[u8],
    start: u32,
    end: u32
) -> Result<(usize, usize)>

Fill buffer at the given interval. If the start coordinate is left of the previous start coordinate, this will use an additional BAM fetch IO operation. Coordinates are 0-based, and end is exclusive. Returns tuple with numbers of added and deleted records since the previous fetch.

pub fn iter(&self) -> Iter<Record>

Iterate over records that have been fetched with fetch.

pub fn iter_mut(&mut self) -> IterMut<Record>

Iterate over mutable references to records that have been fetched with fetch.

pub fn len(&self) -> usize

pub fn is_empty(&self) -> bool

Trait Implementations

impl Debug for RecordBuffer

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

Formats the value using the given formatter.

impl Send for RecordBuffer

impl Sync for RecordBuffer