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// Copyright 2014 Christopher Schröder, Johannes Köster. // Licensed under the MIT license (http://opensource.org/licenses/MIT) // This file may not be copied, modified, or distributed // except according to those terms. //! Rust-Htslib provides a high level API to working with the common HTS file formats. //! //! Htslib itself is the *de facto* standard implementation for reading and writing files for //! HTS alignments (SAM and BAM) as well as variant calls in VCF and BCF format. //! //! For example, reading and writing BAM files is as easy as //! //! ``` //! use rust_htslib::bam; //! use rust_htslib::prelude::*; //! //! let mut bam = bam::Reader::from_path(&"test/test.bam").unwrap(); //! let header = bam::Header::from_template(bam.header()); //! let mut out = bam::Writer::from_path(&"test/out.bam", &header).unwrap(); //! //! // copy reverse reads to new BAM file //! for r in bam.records() { //! let record = r.unwrap(); //! if record.is_reverse() { //! out.write(&record).unwrap(); //! } //! } //! ``` //! //! Pileups can be performed with //! //! ``` //! use rust_htslib::bam; //! use rust_htslib::prelude::*; //! //! let mut bam = bam::Reader::from_path(&"test/test.bam").unwrap(); //! //! // pileup over all covered sites //! for p in bam.pileup() { //! let pileup = p.unwrap(); //! println!("{}:{} depth {}", pileup.tid(), pileup.pos(), pileup.depth()); //! //! for alignment in pileup.alignments() { //! if !alignment.is_del() && !alignment.is_refskip() { //! println!("Base {}", alignment.record().seq()[alignment.qpos().unwrap()]); //! } //! // mark indel start //! match alignment.indel() { //! bam::pileup::Indel::Ins(len) => println!("Insertion of length {} between this and next position.", len), //! bam::pileup::Indel::Del(len) => println!("Deletion of length {} between this and next position.", len), //! bam::pileup::Indel::None => () //! } //! } //! } //! ``` //! //! In both cases, indexed BAM files can be seeked for specific regions, constraining either the record iterator or the pileups: //! //! ``` //! use rust_htslib::bam; //! use rust_htslib::prelude::*; //! //! let mut bam = bam::IndexedReader::from_path(&"test/test.bam").unwrap(); //! //! // seek to chr1:50000-100000 //! let tid = bam.header().tid(b"CHROMOSOME_I").unwrap(); //! bam.fetch(tid, 0, 20).unwrap(); //! // afterwards, read or pileup in this region //! ``` extern crate bitflags; #[macro_use] extern crate custom_derive; extern crate ieee754; extern crate itertools; #[macro_use] extern crate lazy_static; extern crate libc; #[macro_use] extern crate newtype_derive; #[macro_use] extern crate quick_error; extern crate regex; extern crate url; extern crate linear_map; #[cfg(feature = "serde")] extern crate serde; #[cfg(all(test, feature = "serde"))] extern crate bincode; #[cfg(test)] // <-- not needed in examples + integration tests #[macro_use] extern crate pretty_assertions; #[cfg(all(test, feature = "serde"))] extern crate serde_json; pub mod bam; pub mod bcf; pub mod htslib; pub mod prelude; pub mod sam; pub mod tbx; pub mod utils;