Struct BamFile

pub struct BamFile { /* private fields */ }

A BAM/CRAM/SAM File

Implementations

impl BamFile

pub fn set_required_fields(&mut self, flag: u32)

pub fn reference_path<P: AsRef<Path>>(&self, path: P)

Set the path to the reference FAI file. Only used for CRAM

pub fn open<P: AsRef<Path>>(path: P) -> Result<Self, AlignmentError>

Open a BAM/CRAM/SAM file on the disk

pub fn chroms(&self) -> &[(String, usize)]

pub fn range( &mut self, chrom: &str, from: usize, to: usize, ) -> Result<Ranged<'_>, AlignmentError>

Trait Implementations

impl<'a> AlignmentReader<'a> for &'a BamFile

fn start(&self) -> (u32, u32)

fn get_file(&self) -> &'a BamFile

fn next( &self, buf: *mut bam1_t, ) -> Result<Option<Alignment<'a>>, AlignmentError>

fn into_alignment_iter(self) -> AlignmentIter<'a, Self>

where Self: Sized,

impl Drop for BamFile

fn drop(&mut self)

Executes the destructor for this type.