add readme and more friendlier usage instructions

1 files changed, 6 insertions, 3 deletions

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)