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JAL-3130 Attempting to fix 8 tests that pass on a Mac but not on linux (e.g. jv-bamboo)
[jalview.git]
/
test
/
jalview
/
ext
/
htsjdk
/
TestHtsContigDb.java
diff --git
a/test/jalview/ext/htsjdk/TestHtsContigDb.java
b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index
28c5cf0
..
ad9bf03
100644
(file)
--- 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
{
@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));
HtsContigDb db = new HtsContigDb("ADB", new File(pathname));
-
+
assertTrue(db.isValid());
assertTrue(db.isIndexed()); // htsjdk opens the .fai file
assertTrue(db.isValid());
assertTrue(db.isIndexed()); // htsjdk opens the .fai file
-
+
SequenceI sq = db.getSequenceProxy("Deminut");
assertNotNull(sq);
assertEquals(sq.getLength(), 606);
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);
sq = db.getSequenceProxy("PPL_06716");
assertNotNull(sq);
assertEquals(sq.getLength(), 602);
-
+
// dict = db.getDictionary(f, truncate))
}
// dict = db.getDictionary(f, truncate))
}
@@
-73,7
+73,7
@@
public class TestHtsContigDb
expectedExceptions = java.lang.IllegalArgumentException.class)
public final void testGetSequenceProxy_indexed()
{
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");
}
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
{
@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
*/
/*
* create .fai with no overwrite fails if it exists
*/
- try {
+ try
+ {
HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
fail("Expected exception");
} catch (IOException e)
{
HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
fail("Expected exception");
} catch (IOException e)
{
+ System.out.println(
+ "Caught IOException in testCreateFastaSequenceIndex");
+ e.printStackTrace();
// expected
}
// expected
}