Struct Writer

pub struct Writer { /* private fields */ }

A BAM writer.

Implementations

impl Writer

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

Create a new SAM/BAM/CRAM file.

Arguments

• path - the path.
• header - header definition to use
• format - the format to use (SAM/BAM/CRAM)

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

Create a new SAM/BAM/CRAM file at STDOUT.

Arguments

• header - header definition to use
• format - the format to use (SAM/BAM/CRAM)

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

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

Arguments

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

pub fn set_thread_pool(&mut self, tpool: &ThreadPool) -> Result<()>

Use a shared thread-pool for writing. This permits controlling the total thread count when multiple readers and writers are working simultaneously. A thread pool can be created with crate::tpool::ThreadPool::new(n_threads)

Arguments

• tpool - thread pool to use for compression work.

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

Write record to BAM.

Arguments

• record - the record to write

pub fn header(&self) -> &HeaderView

Return the header.

pub fn set_reference<P: AsRef<Path>>(&mut self, path: P) -> Result<()>

Set the reference path for reading CRAM files.

Arguments

• path - path to the FASTA reference

pub fn set_compression_level( &mut self, compression_level: CompressionLevel, ) -> Result<()>

Set the compression level for writing BAM/CRAM files.

Arguments

• compression_level - CompressionLevel enum variant

Trait Implementations

impl Debug for Writer

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

Formats the value using the given formatter.

impl Drop for Writer

fn drop(&mut self)

Executes the destructor for this type.

impl Send for Writer