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//! *bam* is a crate that allows to read and write BAM, SAM and BGZIP files,
//! written completely in Rust.
//!
//! ## Overview
//!
//! Currently, there are three readers and two writers:
//! * [bam::IndexedReader](bam_reader/struct.IndexedReader.html) - fetches records from
//! random genomic regions.
//! * [bam::BamReader](bam_reader/struct.BamReader.html) - reads a BAM file consecutively.
//! * [bam::SamReader](sam/struct.SamReader.html) - reads a SAM file consecutively.
//! * [bam::BamWriter](bam_writer/struct.BamWriter.html) - writes a BAM file.
//! * [bam::SamWriter](sam/struct.SamWriter.html) - writes a SAM file.
//!
//! BAM readers and writers have single-thread and multi-thread modes.
//!
//! You can construct pileups from all readers using [Pileup](pileup/struct.Pileup.html).
//!
//! The [bgzip](bgzip/index.html) module to interact directly with bgzip files (BGZF).
//!
//! The crate also allows to conviniently work with SAM/BAM [records](record/struct.Record.html)
//! and their fields, such as [CIGAR](record/cigar/struct.Cigar.html) or
//! [tags](record/tags/struct.TagViewer.html).
//!
//! ## Usage
//!
//! The following code would load BAM file `in.bam` and its index `in.bam.bai`, take all records
//! from `3:600001-700000` and print them on the stdout.
//!
//! ```rust
//! extern crate bam;
//!
//! use std::io;
//! use bam::RecordWriter;
//!
//! fn main() {
//! let mut reader = bam::IndexedReader::from_path("in.bam").unwrap();
//! let output = io::BufWriter::new(io::stdout());
//! let mut writer = bam::SamWriter::build()
//! .write_header(false)
//! .from_stream(output, reader.header().clone()).unwrap();
//!
//! for record in reader.fetch(&bam::Region::new(2, 600_000, 700_000)).unwrap() {
//! let record = record.unwrap();
//! writer.write(&record).unwrap();
//! }
//! }
//! ```
//!
//! More complicated example with completely created header and record:
//!
//! ```rust
//! extern crate bam;
//!
//! use std::io;
//! use bam::RecordWriter;
//! use bam::header::{Header, HeaderEntry};
//!
//! fn main() {
//! // Creating a header.
//! let mut header = Header::new();
//! // Header line "@HD VN:1.6 SO:Coordinate".
//! let mut header_line = HeaderEntry::header_line("1.6".to_string());
//! header_line.push(b"SO", "Coordinate".to_string());
//! header.push_entry(header_line).unwrap();
//! // Reference line "@SQ SN:chr1 LN:10000".
//! header.push_entry(HeaderEntry::ref_sequence("chr1".to_string(), 10000)).unwrap();
//!
//! // Write SAM to stdout.
//! let output = io::BufWriter::new(io::stdout());
//! let mut writer = bam::SamWriter::from_stream(output, header).unwrap();
//!
//! // Create a new record, set its name to "Read_1",
//! // reference id to 0, start to 10 (both 0-based).
//! let mut record = bam::Record::new();
//! record.set_name("Read_1".bytes());
//! record.set_ref_id(0).unwrap();
//! record.set_start(10).unwrap();
//! // Set the record to be on reverse strand.
//! record.flag_mut().set_strand(false);
//! // Set sequence and qualities (qualities without +33), and cigar.
//! record.set_seq_qual("ACGT".bytes(), [10_u8, 20, 30, 10].iter().cloned()).unwrap();
//! record.set_cigar("2M1I1M".bytes()).unwrap();
//! // Add NM tag.
//! record.tags_mut().push_num(b"NM", 1);
//!
//! writer.write(&record).unwrap();
//! writer.finish().unwrap();
//! // Above code would print the following SAM file:
//! // @HD VN:1.6 SO:Coordinate
//! // @SQ SN:chr1 LN:10000
//! // Read_1 16 chr1 11 0 2M1I1M * 0 0 ACGT +5?+ NM:i:1
//!
//! println!("Aligned pairs:");
//! for (read_pos, ref_pos) in record.aligned_pairs() {
//! println!(" {:?} {:?}", read_pos, ref_pos);
//! }
//! // Aligned pairs:
//! // Some(0) Some(10)
//! // Some(1) Some(11)
//! // Some(2) None
//! // Some(3) Some(12)
//! }
//! ```
extern crate byteorder;
extern crate crc32fast;
extern crate flate2;
pub mod index;
pub mod bgzip;
pub mod record;
pub mod bam_reader;
pub mod bam_writer;
pub mod header;
pub mod sam;
pub mod pileup;
pub use bam_reader::IndexedReader;
pub use bam_reader::BamReader;
pub use bam_reader::Region;
pub use bam_writer::BamWriter;
pub use header::Header;
pub use record::Record;
pub use sam::SamWriter;
pub use sam::SamReader;
pub use pileup::Pileup;
use std::io;
/// A trait for reading BAM/SAM records.
///
/// You can use the single record:
/// ```rust
///let mut record = bam::Record::new();
///loop {
/// // reader: impl RecordReader
/// // New record is saved into record.
/// match reader.read_into(&mut record) {
/// // No more records to read.
/// Ok(false) => break,
/// Ok(true) => {},
/// Err(e) => panic!("{}", e),
/// }
/// // Do somethind with the record.
///}
///```
/// Or you can just iterate over records:
/// ```rust
///for record in reader {
/// let record = record.unwrap();
/// // Do somethind with the record.
///}
///```
pub trait RecordReader: Iterator<Item = io::Result<Record>> {
/// Writes the next record into `record`. It allows to skip excessive memory allocation.
/// If there are no more records to iterate over, the function returns `false`.
///
/// If the function returns an error, the record is cleared.
fn read_into(&mut self, record: &mut Record) -> io::Result<bool>;
/// Pauses multi-thread reader until the next read operation. Does nothing to a single-thread reader.
///
/// Use with caution: pausing and unpausing takes some time.
fn pause(&mut self);
}
/// A trait for writing BAM/SAM records.
pub trait RecordWriter {
/// Writes a single record.
fn write(&mut self, record: &Record) -> io::Result<()>;
/// Finishes the stream, same as `std::mem::drop(writer)`, but can return an error.
fn finish(&mut self) -> io::Result<()>;
/// Flushes contents.
fn flush(&mut self) -> io::Result<()>;
}