From f66ef4626e9d735aeb056366eeaf98cd8b2a1742 Mon Sep 17 00:00:00 2001
From: bthomas <bthomas@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Sep 2010 20:45:51 +0000
Subject: [PATCH] Fixing two minor issues: 1) adding a new error message if the
 user adds a fasta file in a directory that doesn't exist; 2) renaming my
 sample unit tests so they actually run.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/ReferenceDataSource.java         | 10 ++++++++++
 ...taSourceTest.java => SampleDataSourceUnitTest.java} |  4 ++--
 .../sample/{SampleTest.java => SampleUnitTest.java}    |  2 +-
 3 files changed, 13 insertions(+), 3 deletions(-)
 rename java/test/org/broadinstitute/sting/gatk/datasources/sample/{SampleDataSourceTest.java => SampleDataSourceUnitTest.java} (98%)
 rename java/test/org/broadinstitute/sting/gatk/datasources/sample/{SampleTest.java => SampleUnitTest.java} (96%)

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 825131962..cc15f6b01 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
@@ -51,6 +51,16 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
      * @param fastaFile Fasta file to be used as reference
      */
     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.");
+        }
+
         File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
         File dictFile;
         if (fastaFile.getAbsolutePath().endsWith("fa")) {
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
similarity index 98%
rename from java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceTest.java
rename to java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
index e66e6fce3..54b4f0658 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java
@@ -17,13 +17,13 @@ import java.util.Set;
  * Date: Sep 9, 2010
  * Time: 8:21:00 AM
  */
-public class SampleDataSourceTest extends BaseTest {
+public class SampleDataSourceUnitTest extends BaseTest {
 
     // this empty header used to instantiate sampledatasource objects
     private static SAMFileHeader header = new SAMFileHeader();
 
     // all the test sample files are located here
-    private String sampleFilesDir = validationDataLocation +  "sample/";
+    private String sampleFilesDir = validationDataLocation +  "samples/";
 
     // make sure samples are created from the SAM file correctly
     @Test()
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleUnitTest.java
similarity index 96%
rename from java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleTest.java
rename to java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleUnitTest.java
index ce73103e8..9daa55a96 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleUnitTest.java
@@ -11,7 +11,7 @@ import org.junit.Test;
  * Date: Sep 9, 2010
  * Time: 8:21:00 AM
  */
-public class SampleTest extends BaseTest {
+public class SampleUnitTest extends BaseTest {
 
     static Sample sampleA;
     static Sample sampleA1;