Struct rust_htslib::bcf::Writer

source · [−]

pub struct Writer { /* private fields */ }

Expand description

A VCF/BCF writer.

Implementations

source

impl Writer

source

pub fn from_path<P: AsRef<Path>>(
 path: P,
 header: &Header,
 uncompressed: bool,
 format: Format
) -> Result<Self>

Create a new writer that writes to the given path.

Arguments

path - the path
header - header definition to use
uncompressed - disable compression
vcf - write VCF instead of BCF

source

pub fn from_url(
 url: &Url,
 header: &Header,
 uncompressed: bool,
 format: Format
) -> Result<Self>

Create a new writer from a URL.

Arguments

url - the URL
header - header definition to use
uncompressed - disable compression
vcf - write VCF instead of BCF

source

pub fn from_stdout(
 header: &Header,
 uncompressed: bool,
 format: Format
) -> Result<Self>

Create a new writer to stdout.

Arguments

header - header definition to use
uncompressed - disable compression
vcf - write VCF instead of BCF

Obtain reference to the lightweight HeaderView of the BCF header.

source

pub fn empty_record(&self) -> Record

Create empty record for writing to this writer.

This record can then be reused multiple times.

source

pub fn translate(&mut self, record: &mut Record)

Translate record to header of this writer.

Arguments

record - The Record to translate.

source

pub fn subset(&mut self, record: &mut Record)

Subset samples of record to match header of this writer.

Arguments

record - The Record to modify.

source

pub fn write(&mut self, record: &Record) -> Result<()>

Write record to the Writer.

Arguments

record - The Record to write.

source

pub fn set_threads(&mut self, n_threads: usize) -> Result<()>

Activate multi-threaded BCF write support in htslib. This should permit faster writing of large BCF files.

Arguments

n_threads - number of extra background writer threads to use, must be > 0.

Trait Implementations

source

impl Debug for Writer

source

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

Formats the value using the given formatter. Read more

source

impl Drop for Writer

source

fn drop(&mut self)

Executes the destructor for this type. Read more

source

impl Send for Writer

Auto Trait Implementations

impl RefUnwindSafe for Writer

impl !Sync for Writer

impl Unpin for Writer

impl UnwindSafe for Writer

Blanket Implementations

source

impl<T> Any for T where
T: 'static + ?Sized,

source

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

source

impl<T> Borrow<T> for T where
T: ?Sized,

const: unstable · source

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

source

impl<T> BorrowMut<T> for T where
T: ?Sized,

const: unstable · source

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

source

impl<T> From<T> for T

const: unstable · source

fn from(t: T) -> T

Returns the argument unchanged.

source

impl<T, U> Into for T where
U: From<T>,

const: unstable · source

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

source

impl<T, U> TryFrom for T where
U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

source

impl<T, U> TryInto for T where
U: TryFrom<T>,

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

Struct rust_htslib::bcf::Writer

Implementations

impl Writer

pub fn from_path<P: AsRef<Path>>( path: P, header: &Header, uncompressed: bool, format: Format) -> Result<Self>

pub fn from_url( url: &Url, header: &Header, uncompressed: bool, format: Format) -> Result<Self>

pub fn from_stdout( header: &Header, uncompressed: bool, format: Format) -> Result<Self>

pub fn header(&self) -> &HeaderView

pub fn empty_record(&self) -> Record

pub fn translate(&mut self, record: &mut Record)

pub fn subset(&mut self, record: &mut Record)

pub fn write(&mut self, record: &Record) -> Result<()>

pub fn set_threads(&mut self, n_threads: usize) -> Result<()>

Trait Implementations

impl Debug for Writer

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

impl Drop for Writer

fn drop(&mut self)

impl Send for Writer

Auto Trait Implementations

impl RefUnwindSafe for Writer

impl !Sync for Writer

impl Unpin for Writer

impl UnwindSafe for Writer

Blanket Implementations

impl<T> Any for T where T: 'static + ?Sized,

fn type_id(&self) -> TypeId

impl<T> Borrow<T> for T where T: ?Sized,

fn borrow(&self) -> &T

impl<T> BorrowMut<T> for T where T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

impl<T> From<T> for T

fn from(t: T) -> T

impl<T, U> Into<U> for T where U: From<T>,

fn into(self) -> U

impl<T, U> TryFrom<U> for T where U: Into<T>,

type Error = Infallible

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

impl<T, U> TryInto<U> for T where U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

pub fn from_path<P: AsRef<Path>>(
path: P,
header: &Header,
uncompressed: bool,
format: Format
) -> Result<Self>

pub fn from_url(
url: &Url,
header: &Header,
uncompressed: bool,
format: Format
) -> Result<Self>

pub fn from_stdout(
header: &Header,
uncompressed: bool,
format: Format
) -> Result<Self>

impl<T> Any for T where
T: 'static + ?Sized,

impl<T> Borrow<T> for T where
T: ?Sized,

impl<T> BorrowMut<T> for T where
T: ?Sized,

impl<T, U> Into<U> for T where
U: From<T>,

impl<T, U> TryFrom<U> for T where
U: Into<T>,

impl<T, U> TryInto<U> for T where
U: TryFrom<T>,