Merge branch 'develop' into feature-wipereads

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

 package nl.lumc.sasc.biopet.core
 
+import java.util.Properties
+
 object BiopetExecutable {
 
   val modules: Map[String, List[MainCommand]] = Map(
@@ -47,6 +49,9 @@ object BiopetExecutable {
         |
         |%s
         |
+        |Subcommands:
+        |  - version
+        |
         |Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git
       """.stripMargin.format(modules.keys.mkString(","), getVersion, usage)
     }
@@ -69,6 +74,9 @@ object BiopetExecutable {
     }
 
     args match {
+      case Array("version") => {
+          println("version: " + getVersion)
+      }
       case Array(module, name, passArgs @ _*) => {
         getCommand(module, name).main(passArgs.toArray)
       }
@@ -84,6 +92,12 @@ object BiopetExecutable {
   }
   
   def getVersion = {
-    getClass.getPackage.getImplementationVersion
+    getClass.getPackage.getImplementationVersion + " (" + getCommitHash + ")"
+  }
+  
+  def getCommitHash = {
+    val prop = new Properties()
+    prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
+    prop.getProperty("git.commit.id.abbrev")
   }
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

@@ -274,14 +274,16 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
   }
 
   private def createQueueHeader(): Seq[String] = {
-    Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
-      "Copyright (c) 2012 The Broad Institute",
-      "For support and documentation go to http://www.broadinstitute.org/gatk")
+    Seq("Biopet version: " + BiopetExecutable.getVersion,"",
+                     "Based on GATK Queue",
+//                     String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
+                     "Copyright (c) 2012 The Broad Institute",
+                     "For support and documentation go to http://www.broadinstitute.org/gatk")
   }
 
   private def getQueueVersion: String = {
     val stingResources: ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
-
+    
     if (stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version")) {
       stingResources.getString("org.broadinstitute.sting.queue.QueueVersion.version")
     } else {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

@@ -30,9 +30,15 @@ trait ToolCommand extends MainCommand {
           }
         }
     opt[Unit]('h', "help") foreach { _ =>
-      System.err.println(this.usage); sys.exit(1)} text("Print usage")
+      System.err.println(this.usage)
+      sys.exit(1)
+    } text("Print usage")
+    opt[Unit]('v', "version") foreach { _ =>
+      System.err.println("Version: " + BiopetExecutable.getVersion)
+      sys.exit(1)
+    } text("Print version")
   }
-  
+    
   type Args <: AbstractArgs
   type OptParser <: AbstractOptParser