X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;fp=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=28c5cf0ddaf1fe0ca052b08b819129ea1580e336;hb=296593216c47a835f462d1d74a40b41e4818f737;hp=29303d0ee9bc931b3d4504d4039a968d70875d69;hpb=b87ae5ac68939a1b964682046e8b07958fae219a;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 29303d0..28c5cf0 100644
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -78,6 +78,17 @@ public class TestHtsContigDb
     fail("Expected exception opening .fai file");
   }
 
+  /**
+   * Tests that exercise
+   * <ul>
+   * <li>opening an unindexed fasta file</li>
+   * <li>creating a .fai index</li>
+   * <li>opening the fasta file, now using the index</li>
+   * <li>error on creating index if overwrite not allowed</li>
+   * </ul>
+   * 
+   * @throws IOException
+   */
   @Test(groups = "Functional")
   public void testCreateFastaSequenceIndex() throws IOException
   {
@@ -120,4 +131,18 @@ public class TestHtsContigDb
     assertTrue(db.isIndexed());
     db.close();
   }
+
+  /**
+   * A convenience 'test' that may be run to create a .fai file for any given
+   * fasta file
+   * 
+   * @throws IOException
+   */
+  @Test(enabled = false)
+  public void testCreateIndex() throws IOException
+  {
+
+    File fasta = new File("test/jalview/io/vcf/contigs.fasta");
+    HtsContigDb.createFastaSequenceIndex(fasta.toPath(), true);
+  }
 }