From ec911ce5bb8c3873dbfd0a0eb409aaed5d6a82a6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 17 Oct 2011 15:27:22 -0400
Subject: [PATCH] Even better error messages

---
 .../sting/commandline/ArgumentTypeDescriptor.java           | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 14275c57b..b54e7c7b1 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -379,8 +379,10 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                     }
 
                     if ( tribbleType == null )
-                        if ( ! file.canRead() | ! file.isFile() ) {
-                            throw new UserException.CouldNotReadInputFile(file, "file does't exist or couldn't be read");
+                        if ( ! file.exists() ) {
+                            throw new UserException.CouldNotReadInputFile(file, "file does not exist");
+                        } else if ( ! file.canRead() | ! file.isFile() ) {
+                            throw new UserException.CouldNotReadInputFile(file, "file could not be read");
                         } else {
                             throw new UserException.CommandLineException(
                                     String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +