#+title: Bam2Seq

[[https://crates.io/crates/bam2seq][https://img.shields.io/crates/v/bam2seq.svg]]
[[https://crates.io/crates/bam2seq][https://img.shields.io/crates/d/bam2seq.svg]]

This tool takes a BAM file containing CIGAR strings, reads, and ~MD~ tags,
and outputs a ~.seq~ file containing pairs of reads and reconstructed references.

** Installation

Install directly with cargo from [[https://crates.io/crates/bam2seq][crates.io]]:
#+begin_src
cargo install bam2seq
#+end_src

Simply clone the repository, and optionally install the binary.
#+begin_src
git clone https://github.com/ragnargrootkoerkamp/bam2seq.git
cd bam2seq
cargo install --path .
#+end_src

** Usage
#+begin_src
cargo run --release -- <input.bam> [<output.seq>] [--no-clip] [--min-len <len>]
#+end_src

- ~input.bam~ :: The input BAM file.
- ~output.seq~ :: The output ~.seq~ file. Defaults to ~input.seq~.
- ~--no-clip~ :: Disable trimming of soft clipped regions from the read.
- ~--min-len <len>~ :: Only output (clipped) reads of at least this length.

This outputs a ~.seq~ file, which looks like this:
#+begin_src
>ACTGATGA
<ACAGATG
>read 2
<reference 2
...
#+end_src

** Links

- This is quite similar to [[https://github.com/mlafave/sam2pairwise][sam2pairwise]] but writes a simpler output format.
- All the work in the implementation is done by the [[https://docs.rs/bam/latest/bam/][BAM]] crate.