This is a reimplementation of Xenomapper [1] in Haskell.  Unlike the
orginal it is significantly more focused in scope: only primary specific
alignments are output.

Example usage: "xenomapper output.bam primary-input.bam secondary-input.bam"

The first argument is the output bam path, and the subsequent are the
primary and secondary alignments. NB: the inputs must be name sorted
and the output will be name sorted.

Building the binary requires a flake enabled Nix [2]. Run

  nix build git://vk3.wtf/xenomapper-hs.git

to build, or if you have already cloned the repository then simply

  nix build

in the root. You can also just:

  nix run git://vk3.wtf/xenomapper-hs.git output.bam primary-input.bam secondary-input.bam

--
1: https://github.com/genomematt/xenomapper
2: https://nixos.org/Nix