Struct rust_htslib::bcf::Writer

pub struct Writer { /* fields omitted */ }

A VCF/BCF writer.

Methods

impl Writer

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

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

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

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

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

Create a new writer to stdout.

Arguments

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

pub fn header(&self) -> &HeaderView

Obtain reference to the lightweight HeaderView of the BCF header.

pub fn empty_record(&self) -> Record

Create empty record for writing to this writer.

This record can then be reused multiple times.

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

Translate record to header of this writer.

Arguments

• record - The Record to translate.

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

Subset samples of record to match header of this writer.

Arguments

• record - The Record to modify.

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

Write record to the Writer.

Arguments

• record - The Record to write.

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

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

impl Debug for Writer

fn fmt(&self, __arg_0: &mut Formatter) -> Result

Formats the value using the given formatter.

impl Send for Writer

impl Drop for Writer

fn drop(&mut self)

Executes the destructor for this type.