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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
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