From 9498950b1c02cd77a2ab4a539f76a8f2ce2724c3 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Thu, 3 Oct 2013 16:52:48 -0400
Subject: [PATCH] Adding more specific error message when one of the scripts
 doesn't exist. --Previously it gave a cryptic message: ----IO error while
 decoding blarg.script with UTF-8 ----Please try specifying another one using
 the -encoding option

---
 .../src/org/broadinstitute/sting/queue/QScriptManager.scala | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
index c6b8eff13..80dd53302 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
@@ -36,6 +36,7 @@ import org.apache.log4j.Level
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
 import org.broadinstitute.sting.utils.classloader.JVMUtils
 import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
+import org.broadinstitute.sting.utils.exceptions.UserException
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -46,6 +47,11 @@ class QScriptManager() extends Logging {
    * Heavily based on scala/src/compiler/scala/tools/ant/Scalac.scala
    */
   def loadScripts(scripts: Seq[File], tempDir: File) {
+    // Make sure the scripts actually exist.
+    scripts.foreach{
+        file => if( !file.exists()) throw new UserException.CouldNotReadInputFile(file, "it does not exist.")
+    }
+
     if (scripts.size > 0) {
       val settings = new Settings((error: String) => logger.error(error))
       settings.deprecation.value = true