From 250c18e679648360c4ee21ddeb0e60b385b25aac Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 5 Oct 2010 03:37:13 +0000
Subject: [PATCH] Error message fixes for the following issues:

nvjpM4yOwQAu3fNGxi4oXLuVpKn6aAlf,1GL0OuXK2xKQfvbu34tWYgbojSVSLo0l,
ehEGBJOfgc4V7qj8W0Homf5ICuVK5Sm3,cZsreLm1CbY3aYKZhV7DOSvQNwur41zp,
GlrlyGEyP9kJDIRCQNFQp7BGJBXSzdDJ,hyz1uiHXr39ANmdZu9K1epOSX8EL3mDw,
q0n4EucZESCI4LZhQik306zD4VAuH2cb.

Messages:
camrhG5tHzlY9WUSEVpVZGkU1tyJqKb5,s0OX2g7nYRctJxyFoQCa6clac9IsjHyi,
THIAtjllvYNlnTmiMnJEIHd2Ju4gqQIO,jwVk3JYZJNHloW7HO4LeGxFexknqro0v,
BFNRGOGmGGJNNPZqgeF1ikTNFfskbyLc,...

Were fixed in 4392.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4428 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../reference/FastaSequenceIndexBuilder.java       |  2 +-
 .../sting/gatk/GenomeAnalysisEngine.java           |  3 ++-
 .../simpleDataSources/ReferenceDataSource.java     | 14 +++++++-------
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
index 45b190537..6f143ed89 100644
--- a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
+++ b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
@@ -212,7 +212,7 @@ public class FastaSequenceIndexBuilder {
             return sequenceIndex;
         }
         catch (IOException e) {
-            throw new UserException.CouldNotReadInputFile(fastaFile, String.format("Could not read fasta file"), e);
+            throw new UserException.CouldNotReadInputFile(fastaFile, "Could not read fasta file", e);
         }
         catch (Exception e) {
             throw new ReviewedStingException(e.getMessage(), e);
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 2a1de19c1..fd1fdc4ea 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -240,7 +240,8 @@ public class GenomeAnalysisEngine extends AbstractGenomeAnalysisEngine {
                     found = true;
             }
             if (!found)
-                throw new ArgumentException(String.format("Unable to find reference metadata (%s,%s)", required.name(), required.type()));
+                throw new ArgumentException(String.format("Walker requires reference metadata to be supplied named '%s' of type '%s', but this metadata was not provided.  " +
+                                                          "Please supply the specified metadata file.", required.name(), required.type().getSimpleName()));
         }
 
         // Check to see that no forbidden rods are present.
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
index cc15f6b01..90b7420c5 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
@@ -30,6 +30,7 @@ import net.sf.picard.reference.FastaSequenceIndexBuilder;
 import net.sf.picard.sam.CreateSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.FastaSequenceIndex;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.file.FSLockWithShared;
 import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
@@ -53,13 +54,8 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
     public ReferenceDataSource(File fastaFile) {
 
         // does the fasta file exist? check that first...
-        if (!fastaFile.exists()) {
-            if (!fastaFile.getParentFile().exists())
-                throw new UserException("The fasta file path you provided is invalid. The directory " +
-                       fastaFile.getParentFile().getAbsolutePath() + " does not exist." );
-            else
-                throw new UserException("The fasta file you provided does not exist.");
-        }
+        if (!fastaFile.exists())
+            throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist.");
 
         File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
         File dictFile;
@@ -89,6 +85,10 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
                 logger.info("Unable to create write lock: " + ex.getMessage());
                 logger.info("Skipping index creation.");
             }
+            catch(UserException e) {
+                // Rethrow all user exceptions as-is; there should be more details in the UserException itself. 
+                throw e;    
+            }
             catch (Exception e) {
                 // If lock creation succeeded, the failure must have been generating the index.
                 // If lock creation failed, just skip over index creation entirely.