Struct BamReader 

pub struct BamReader { /* private fields */ }

Implementations

impl BamReader

pub fn open( path: &str, index_path: Option<&str>, parallel: i64, block_size: Option<u64>, max_blocks: Option<usize>, ) -> Result<Self>

pub fn header(&self) -> &SamHeader

pub fn chr_sizes(&self) -> &ChrMap

pub fn index_error(&self) -> &str

pub fn is_indexed(&self) -> bool

pub fn is_closed(&self) -> bool

pub fn path(&self) -> &str

pub fn parallel(&self) -> usize

pub fn close(&mut self)

pub fn read_entries(&self, req: &EntriesRequest) -> Result<Vec<Vec<BamRecord>>>

One list per locus, in the order the loci were given.

Each locus gets its own full list, so two overlapping loci both report the alignments they share.

pub fn read_all_entries(&self, req: &EntriesRequest) -> Result<Vec<BamRecord>>

Every alignment on the named references, in reference then coordinate order.

Unplaced alignments are left out: the index reaches an alignment only through the reference it sits on.

pub fn iter_entries(&self, req: &EntriesRequest) -> Result<LocusEntries<'_>>

Per-locus, lazily.

pub fn iter_all_entries( &self, req: &EntriesRequest, window: i64, ) -> Result<WindowEntries<'_>>

Successive windows over whole references.

A window never spans two references, and an alignment reaching over a boundary is reported by the window it starts in.

Trait Implementations

impl Debug for BamReader

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

Formats the value using the given formatter.