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 +++++++++++++++++++++++
 xenomapper.hs |  9 ++++++---
 2 files changed, 29 insertions(+), 3 deletions(-)
 create mode 100644 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
diff --git a/xenomapper.hs b/xenomapper.hs
index 123b1a5..4546ab2 100644
--- a/xenomapper.hs
+++ b/xenomapper.hs
@@ -36,6 +36,9 @@ filterBams a b = do
 
 main = do
   args <- getArgs
-
-  withLogging_ (LoggingConf Warning Error Error 10 True) $ do
-    decodeBamFiles args (\[(hdr, prim), (_, sec)] -> writeBamFile "primary.bam" hdr $ filterBams prim sec)
+  if length args /= 3 then do
+    path <- getProgName
+    hPutStrLn stderr $ unwords [ "usage:", path, "output.bam", "input1.bam", "input2.bam" ]
+  else
+    withLogging_ (LoggingConf Warning Error Error 10 True) $ do
+      decodeBamFiles (tail args) (\[(hdr, prim), (_, sec)] -> writeBamFile (head args) hdr $ filterBams prim sec)
-- 
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