From c10cfb984d3a0881458018325e2b95219ed16829 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 29 Jul 2021 17:03:11 +1000
Subject: add readme and more friendlier usage instructions

---
 README | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 README

(limited to 'README')

diff --git a/README b/README
new file mode 100644
index 0000000..87b50ee
--- /dev/null
+++ b/README
@@ -0,0 +1,23 @@
+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-hs primary-specific.bam primary.bam secondary.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.
+
+--
+1: https://github.com/genomematt/xenomapper
+2: https://nixos.org/Nix
-- 
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