+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 -- [] [--no-clip] [--min-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 ~ :: Only output (clipped) reads of at least this length.

This outputs a ~.seq~ file, which looks like this:

+begin_src

ACTGATGA

+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.