Enum Alignments 

pub enum Alignments {
    Bam(BamReader),
    Cram(CramReader),
}

A BAM or a CRAM, opened for reading.

Variants

Bam(BamReader)

Cram(CramReader)

Implementations

impl Alignments

pub fn kind(&self) -> &'static str

"bam" or "cram".

pub fn header(&self) -> &SamHeader

pub fn chr_sizes(&self) -> &ChrMap

pub fn is_indexed(&self) -> bool

pub fn index_error(&self) -> &str

pub fn is_closed(&self) -> bool

pub fn path(&self) -> &str

pub fn parallel(&self) -> usize

pub fn close(&mut self)

pub fn version(&self) -> Option<(u8, u8)>

The CRAM version, or None for a BAM.

pub fn reference_path(&self) -> Option<&str>

The reference FASTA in use. Always None for a BAM, which needs none.

pub fn reference_error(&self) -> &str

Why there is no reference, when there is none and one was wanted.

pub fn read_entries(&self, req: &EntriesRequest) -> Result<Vec<Vec<BamRecord>>>

pub fn read_all_entries(&self, req: &EntriesRequest) -> Result<Vec<BamRecord>>

Trait Implementations

impl Debug for Alignments

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

Formats the value using the given formatter.