Struct CramReader 

pub struct CramReader { /* private fields */ }

Implementations

impl CramReader

pub fn open( path: &str, index_path: Option<&str>, reference: 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 version(&self) -> (u8, u8)

The CRAM version, as (major, minor).

pub fn reference_path(&self) -> Option<&str>

The reference in use, or None when none resolved.

pub fn reference_error(&self) -> &str

Why there is no reference, when there is none. Empty when one resolved.

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.

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

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

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.

Trait Implementations

impl Debug for CramReader

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

Formats the value using the given formatter.