From 81532a05298b8bd2b4faf32a9360c726f8f0eb59 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 12 Oct 2012 09:48:12 -0400
Subject: [PATCH] Missing file are user errors.

---
 .../gatk/datasources/rmd/ReferenceOrderedDataSource.java      | 4 ++++
 .../broadinstitute/sting/utils/exceptions/UserException.java  | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
index 5b4be2fc6..664d96321 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
@@ -34,8 +34,10 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.lang.reflect.Type;
 import java.util.List;
@@ -239,6 +241,8 @@ class ReferenceOrderedQueryDataPool extends ResourcePool<RMDTrack,LocationAwareS
             } else {
                 return new SeekableRODIterator(header,sequenceDictionary,referenceSequenceDictionary,genomeLocParser,track.getIterator());
             }
+        } catch (FileNotFoundException e) {
+            throw new UserException.CouldNotReadInputFile(fileDescriptor.getName(), "it could not be found");
         } catch (IOException e) {
             throw new ReviewedStingException("Unable to create iterator for rod named " + fileDescriptor.getName(),e);
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index eaa8d7943..6b97f8f9f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -166,6 +166,10 @@ public class UserException extends ReviewedStingException {
             super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message));
         }
 
+        public CouldNotReadInputFile(String file, String message) {
+            super(String.format("Couldn't read file %s because %s", file, message));
+        }
+
         public CouldNotReadInputFile(File file, String message, Exception e) {
             super(String.format("Couldn't read file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
         }