Added text to cmdArgs

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala

@@ -29,19 +29,19 @@ object BamStats extends ToolCommand {
   class OptParser extends AbstractOptParser {
     opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
       c.copy(referenceFasta = Some(x))
-    }
+    } text "Fasta file of reference"
     opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
       c.copy(outputDir = x)
-    }
+    } text "Output directory"
     opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
       c.copy(bamFile = x)
-    }
+    } text "Input bam file"
     opt[Int]("binSize") valueName "<int>" action { (x, c) =>
       c.copy(binSize = x)
-    }
+    } text "Bin size of stats (beta)"
     opt[Int]("threadBinSize") valueName "<int>" action { (x, c) =>
       c.copy(threadBinSize = x)
-    }
+    } text "Size of region per thread"
   }
 
   /** This is the main entry to [[BamStats]], this will do the argument parsing. */