+title: Bam2Seq

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

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 -- [--clip] [--min-len ]

+end_src

• ~--clip~ :: If the CIGAR string contains ~S~ at the start/end, remove the first/last ~~ characters 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.