[−][src]Struct rust_htslib::bam::Reader
A BAM reader.
Methods
impl Reader
[src]
pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Self>
[src]
pub fn from_stdin() -> Result<Self>
[src]
Create a new Reader from STDIN.
pub fn from_url(url: &Url) -> Result<Self>
[src]
Create a new Reader from URL.
pub fn iter_chunk(
&mut self,
start: Option<i64>,
end: Option<i64>
) -> ChunkIterator<Self>
[src]
&mut self,
start: Option<i64>,
end: Option<i64>
) -> ChunkIterator<Self>
Iterator over the records between the (optional) virtual offsets start
and end
Arguments
-
start
- Optional starting virtual offset to seek to. Throws an error if it is not a valid virtual offset. -
end
- Read until the virtual offset is less thanend
pub fn set_reference<P: AsRef<Path>>(&mut self, path: P) -> Result<()>
[src]
Trait Implementations
impl Debug for Reader
[src]
impl Drop for Reader
[src]
impl Read for Reader
[src]
fn read(&mut self, record: &mut Record) -> Result<bool>
[src]
Read the next BAM record into the given Record
.
Returns a true result if a record was read, or false if there are no more records.
This method is useful if you want to read records as fast as possible as the
Record
can be reused. A more ergonomic approach is to use the records
iterator.
Errors
If there are any issues with reading the next record an error will be returned.
Examples
use rust_htslib::bam::{Error, Read, Reader, Record}; let mut bam = Reader::from_path(&"test/test.bam")?; let mut record = Record::new(); // Print the TID of each record while bam.read(&mut record)? { println!("TID: {}", record.tid()) }
fn records(&mut self) -> Records<Self>
[src]
Iterator over the records of the fetched region.
Note that, while being convenient, this is less efficient than pre-allocating a
Record
and reading into it with the read
method, since every iteration involves
the allocation of a new Record
.
fn pileup(&mut self) -> Pileups<Self>
[src]
fn htsfile(&self) -> *mut htsFile
[src]
fn header(&self) -> &HeaderView
[src]
fn header_mut(&mut self) -> &mut HeaderView
[src]
fn seek(&mut self, offset: i64) -> Result<()>
[src]
fn tell(&self) -> i64
[src]
fn set_threads(&mut self, n_threads: usize) -> Result<()>
[src]
impl Send for Reader
[src]
Auto Trait Implementations
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized,
[src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized,
[src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
[src]
T: ?Sized,
fn borrow_mut(&mut self) -> &mut T
[src]
impl<T> From<T> for T
[src]
impl<T, U> Into<U> for T where
U: From<T>,
[src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>,
[src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
[src]
U: TryFrom<T>,