Trait rust_htslib::bam::Read

pub trait Read: Sized {
    // Required methods
    fn read(&mut self, record: &mut Record) -> Option<Result<()>>;
    fn records(&mut self) -> Records<'_, Self> ;
    fn rc_records(&mut self) -> RcRecords<'_, Self> ;
    fn pileup(&mut self) -> Pileups<'_, Self> ;
    fn htsfile(&self) -> *mut htsFile;
    fn header(&self) -> &HeaderView;
    fn set_thread_pool(&mut self, tpool: &ThreadPool) -> Result<()>;

    // Provided methods
    fn seek(&mut self, offset: i64) -> Result<()> { ... }
    fn tell(&self) -> i64 { ... }
    fn set_threads(&mut self, n_threads: usize) -> Result<()> { ... }
    fn set_cram_options(
        &mut self,
        fmt_opt: hts_fmt_option,
        fields: sam_fields
    ) -> Result<()> { ... }
}

A trait for a BAM reader with a read method.

Required Methods

fn read(&mut self, record: &mut Record) -> Option<Result<()>>

Read next BAM record into given record. Use this method in combination with a single allocated record to avoid the reallocations occurring with the iterator.

Arguments

• record - the record to be filled

Returns

Some(Ok(())) if the record was read and None if no more records to read

Example:

use rust_htslib::errors::Error;
use rust_htslib::bam::{Read, IndexedReader, Record};

let mut bam = IndexedReader::from_path(&"test/test.bam").unwrap();
bam.fetch((0, 1000, 2000)); // reads on tid 0, from 1000bp to 2000bp
let mut record = Record::new();
while let Some(result) = bam.read(&mut record) {
    match result {
        Ok(_) => {
            println!("Read sequence: {:?}", record.seq().as_bytes());
        }
        Err(_) => panic!("BAM parsing failed...")
    }
}

Consider using rc_records instead.

fn records(&mut self) -> Records<'_, Self>

Iterator over the records of the seeked region. Note that, while being convenient, this is less efficient than pre-allocating a Record and reading into it with the read method, since every iteration involves the allocation of a new Record.

This is about 10% slower than record in micro benchmarks.

Consider using rc_records instead.

fn rc_records(&mut self) -> RcRecords<'_, Self>

Records iterator using an Rc to avoid allocating a Record each turn. This is about 1% slower than the read based API in micro benchmarks, but has nicer ergonomics (and might not actually be slower in your applications).

Example:

use rust_htslib::errors::Error;
use rust_htslib::bam::{Read, Reader, Record};
use rust_htslib::htslib; // for BAM_F*
let mut bam = Reader::from_path(&"test/test.bam").unwrap();

for read in
    bam.rc_records()
    .map(|x| x.expect("Failure parsing Bam file"))
    .filter(|read|
        read.flags()
         & (htslib::BAM_FUNMAP
             | htslib::BAM_FSECONDARY
             | htslib::BAM_FQCFAIL
             | htslib::BAM_FDUP) as u16
         == 0
    )
    .filter(|read| !read.is_reverse()) {
    println!("Found a forward read: {:?}", read.qname());
}

//or to add the read qnames into a Vec
let collected: Vec<_> = bam.rc_records().map(|read| read.unwrap().qname().to_vec()).collect();

fn pileup(&mut self) -> Pileups<'_, Self>

Iterator over pileups.

fn htsfile(&self) -> *mut htsFile

Return the htsFile struct

fn header(&self) -> &HeaderView

Return the header.

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.

Provided Methods

fn seek(&mut self, offset: i64) -> Result<()>

Seek to the given virtual offset in the file

fn tell(&self) -> i64

Report the current virtual offset

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

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

Setting nthreads to 0 does not change the current state. Note that it is not possible to set the number of background threads below 1 once it has been set.

Arguments

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

fn set_cram_options( &mut self, fmt_opt: hts_fmt_option, fields: sam_fields ) -> Result<()>

If the underlying file is in CRAM format, allows modifying CRAM options. Note that this method does not check that the underlying file actually is in CRAM format.

Examples

Set the required fields to RNAME and FLAG, potentially allowing htslib to skip over the rest, resulting in faster iteration:

use rust_htslib::bam::{Read, Reader};
use hts_sys;
let mut cram = Reader::from_path(&"test/test_cram.cram").unwrap();
cram.set_cram_options(hts_sys::hts_fmt_option_CRAM_OPT_REQUIRED_FIELDS,
            hts_sys::sam_fields_SAM_RNAME | hts_sys::sam_fields_SAM_FLAG).unwrap();

Object Safety

This trait is not object safe.

Implementors

impl Read for IndexedReader

impl Read for Reader