X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=ad9bf0342ff180e766ff2ba9b360eeb953e0503f;hb=dcdf54b52932630bbc230a6e553db0a7482a2cb4;hp=28c5cf0ddaf1fe0ca052b08b819129ea1580e336;hpb=37e53fb916ef469eda6fd042701e116d56ff3c0b;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 28c5cf0..ad9bf03 100644
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -44,12 +44,12 @@ public class TestHtsContigDb
   @Test(groups = "Functional")
   public final void testGetSequenceProxy() throws Exception
   {
-    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta";
+    String pathname = "test/jalview/ext/htsjdk/pgmB.fasta";
     HtsContigDb db = new HtsContigDb("ADB", new File(pathname));
-    
+
     assertTrue(db.isValid());
     assertTrue(db.isIndexed()); // htsjdk opens the .fai file
-    
+
     SequenceI sq = db.getSequenceProxy("Deminut");
     assertNotNull(sq);
     assertEquals(sq.getLength(), 606);
@@ -60,7 +60,7 @@ public class TestHtsContigDb
     sq = db.getSequenceProxy("PPL_06716");
     assertNotNull(sq);
     assertEquals(sq.getLength(), 602);
-    
+
     // dict = db.getDictionary(f, truncate))
   }
 
@@ -73,7 +73,7 @@ public class TestHtsContigDb
     expectedExceptions = java.lang.IllegalArgumentException.class)
   public final void testGetSequenceProxy_indexed()
   {
-    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai";
+    String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai";
     new HtsContigDb("ADB", new File(pathname));
     fail("Expected exception opening .fai file");
   }
@@ -92,16 +92,20 @@ public class TestHtsContigDb
   @Test(groups = "Functional")
   public void testCreateFastaSequenceIndex() throws IOException
   {
-    File fasta = new File("test/jalview/ext/htsjdk/pgmb.fasta");
-    
+    File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta");
+
     /*
      * create .fai with no overwrite fails if it exists
      */
-    try {
+    try
+    {
       HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
       fail("Expected exception");
     } catch (IOException e)
     {
+      System.out.println(
+              "Caught IOException in testCreateFastaSequenceIndex");
+      e.printStackTrace();
       // expected
     }