Merge pull request #370 from AdamaJava/qbasepileup_mt

fix(qbasepileup): chrM was automatically changed to chrMT

Author: newellf

qbasepileup/src/org/qcmg/qbasepileup/QBasePileupUtil.java

@@ -39,17 +39,9 @@ public static String getFullChromosome(String ref) {
 
 		// if ref starts with chr or GL, just return it
 		if (ref.startsWith("chr") || ref.startsWith("GL")) {
-			if (ref.equals("chrM")) {
-				return "chrMT";
-			}
 			return ref;
 		}
 
-		
-		if (ref.equals("M")) {
-			return "chrMT";
-		}
-		
 		if (addChromosomeReference(ref)) {
 			return "chr" + ref;
 		} else {

qbasepileup/test/org/qcmg/qbasepileup/QBasePileupUtilTest.java

@@ -16,7 +16,7 @@ public void testGetFullChromosome() {
 
 		assertEquals("chr10", QBasePileupUtil.getFullChromosome("10"));
 		assertEquals("chr10", QBasePileupUtil.getFullChromosome("chr10"));
-		assertEquals("chrMT", QBasePileupUtil.getFullChromosome("M"));
+		assertEquals("chrM", QBasePileupUtil.getFullChromosome("M"));
 		assertEquals("chrMT", QBasePileupUtil.getFullChromosome("MT"));
 		assertEquals("GL12345", QBasePileupUtil.getFullChromosome("GL12345"));
 	}

qbasepileup/test/org/qcmg/qbasepileup/snp/SnpPositionTest.java

@@ -50,9 +50,9 @@ public void testEquals() throws QBasePileupException {
 	}
 
 	@Test
-	public void doesMurnIntochrMT() {
+	public void doesMurnIntochrM() {
 		SnpPosition p = new SnpPosition("test", "M", 1234, 1235);
-		assertEquals("chrMT", p.getFullChromosome());
+		assertEquals("chrM", p.getFullChromosome());
 	}
 	@Test
 	public void doesMTurnIntochrMT() {