diff options
Diffstat (limited to 'xenomapper.hs')
| -rw-r--r-- | xenomapper.hs | 9 |
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) |