Struct SamReader 

pub struct SamReader { /* private fields */ }

SAM file reader (streaming, memory-efficient)

Implementations

impl SamReader

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Self>

Open a SAM file from a path - handles .sam and .sam.gz automatically

pub fn new<R: BufRead + 'static>(reader: R) -> Self

Create a new SAM reader from any BufRead source

pub fn read_header(&mut self) -> Result<&SamHeader>

Read and parse the SAM header

This must be called before reading records. Header lines start with ‘@’, record lines don’t.

pub fn header(&self) -> Option<&SamHeader>

Get the header (must call read_header first)

pub fn compute_stats(self, _config: Option<ParallelConfig>) -> Result<SamStats>

Compute statistics from this reader

Trait Implementations

impl GenomicReader for SamReader

type Metadata = SamHeader

Metadata type for this reader

fn metadata(&self) -> &Self::Metadata

Get metadata about the genomic data (headers, contigs, etc.)

impl GenomicRecordIterator for SamReader

type Record = SamRecord

The record type yielded by this iterator

fn next_raw(&mut self) -> Result<Option<Vec<u8>>>

Advance to the next raw record

fn next_record(&mut self) -> Result<Option<Self::Record>>

Advance to the next record

fn collect_all(self) -> Result<Vec<Self::Record>>

where Self: Sized,

Consume the iterator and collect all records into a vector

fn chunks(self, chunk_size: usize) -> ChunkedIterator<Self>

where Self: Sized,

Process records in chunks for memory-efficient batch operations