Revert "test (double,double) assertions made compatible with future t…

…est framework"

This reverts commit fd8b16d.

src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java

@@ -520,7 +520,7 @@ public void testPctRibosomalBases() throws Exception {
 
         final RnaSeqMetrics metrics = output.getMetrics().get(0);
 
-        Assert.assertEquals(metrics.PCT_RIBOSOMAL_BASES.doubleValue(), 0.4);
+        Assert.assertEquals(metrics.PCT_RIBOSOMAL_BASES, 0.4);
     }
 
     public File getRefFlatFile(String sequence, String txStart, String txEnd, String cdsStart, String cdsEnd, String exonCount, String exonStarts, String exonEnds) throws Exception {

src/test/java/picard/analysis/MergeableMetricBaseTest.java

@@ -200,13 +200,13 @@ public void testMerging() {
         Assert.assertEquals(metric1.boxedInt, (Integer) 2);
         Assert.assertEquals(metric1.unboxedInt, 4);
 
-        Assert.assertEquals(metric1.boxedDouble.doubleValue(), 6D);
+        Assert.assertEquals(metric1.boxedDouble, 6D);
         Assert.assertEquals(metric1.unboxedDouble, 8D);
 
         Assert.assertEquals(metric1.boxedLong, (Long) 10L);
         Assert.assertEquals(metric1.unboxedLong, 12L);
 
-        Assert.assertEquals(metric1.boxedFloat.floatValue(), 14F);
+        Assert.assertEquals(metric1.boxedFloat, 14F);
         Assert.assertEquals(metric1.unboxedFloat, 16F);
 
         Assert.assertEquals(metric1.boxedShort, (Short) (short) 18);

src/test/java/picard/analysis/TheoreticalSensitivityTest.java

@@ -71,15 +71,15 @@ public void testProportionsAboveThresholds() throws Exception {
         final List<ArrayList<Double>> proportions = TheoreticalSensitivity.proportionsAboveThresholds(sums, thresholds);
         Assert.assertEquals(proportions.size(), 3);
 
-        Assert.assertEquals(proportions.get(0).get(0).doubleValue(), (double) 3 / 3);
-        Assert.assertEquals(proportions.get(0).get(1).doubleValue(), (double) 0 / 3);
-        Assert.assertEquals(proportions.get(0).get(2).doubleValue(), (double) 0 / 3);
-        Assert.assertEquals(proportions.get(1).get(0).doubleValue(), (double) 2 / 2);
-        Assert.assertEquals(proportions.get(1).get(1).doubleValue(), (double) 2 / 2);
-        Assert.assertEquals(proportions.get(1).get(2).doubleValue(), (double) 2 / 2);
-        Assert.assertEquals(proportions.get(2).get(0).doubleValue(), (double) 3 / 4);
-        Assert.assertEquals(proportions.get(2).get(1).doubleValue(), (double) 3 / 4);
-        Assert.assertEquals(proportions.get(2).get(2).doubleValue(), (double) 1 / 4);
+        Assert.assertEquals(proportions.get(0).get(0), (double) 3 / 3);
+        Assert.assertEquals(proportions.get(0).get(1), (double) 0 / 3);
+        Assert.assertEquals(proportions.get(0).get(2), (double) 0 / 3);
+        Assert.assertEquals(proportions.get(1).get(0), (double) 2 / 2);
+        Assert.assertEquals(proportions.get(1).get(1), (double) 2 / 2);
+        Assert.assertEquals(proportions.get(1).get(2), (double) 2 / 2);
+        Assert.assertEquals(proportions.get(2).get(0), (double) 3 / 4);
+        Assert.assertEquals(proportions.get(2).get(1), (double) 3 / 4);
+        Assert.assertEquals(proportions.get(2).get(2), (double) 1 / 4);
     }
 
     @Test
@@ -93,7 +93,7 @@ public void testHetAltDepthDistribution() throws Exception {
 
                 final long binomialCoefficient = CombinatoricsUtils.binomialCoefficient(n, m);
 
-                Assert.assertEquals(distribution.get(n).get(m).doubleValue(), binomialCoefficient * Math.pow(p, n));
+                Assert.assertEquals(distribution.get(n).get(m), binomialCoefficient * Math.pow(p, n));
             }
         }
     }

src/test/java/picard/arrays/illumina/InfiniumVcfFieldsTest.java

@@ -24,7 +24,7 @@ public void testGetValueFromVcfOtherHeaderLine() throws ParseException {
             Assert.assertEquals(InfiniumVcfFields.getOptionalValueFromVcfOtherHeaderLine(header, InfiniumVcfFields.PIPELINE_VERSION), "IlluminaGenotypingArray_v1.5");
             Assert.assertEquals(InfiniumVcfFields.getIntegerFromVcfOtherHeaderLine(header, InfiniumVcfFields.ANALYSIS_VERSION_NUMBER).intValue(), 1);
             Assert.assertEquals(InfiniumVcfFields.getValueFromVcfOtherHeaderLine(header, InfiniumVcfFields.EXTENDED_ILLUMINA_MANIFEST_VERSION), "1.3");
-            Assert.assertEquals(InfiniumVcfFields.getOptionalDoubleFromVcfOtherHeaderLine(header, InfiniumVcfFields.GTC_CALL_RATE).doubleValue(), 0.985);
+            Assert.assertEquals(InfiniumVcfFields.getOptionalDoubleFromVcfOtherHeaderLine(header, InfiniumVcfFields.GTC_CALL_RATE), 0.985);
             Assert.assertEquals(InfiniumVcfFields.getOptionalValueFromVcfOtherHeaderLine(header, InfiniumVcfFields.AUTOCALL_GENDER), "M");
             Assert.assertNull(InfiniumVcfFields.getOptionalValueFromVcfOtherHeaderLine(header, "nothing"));
             Assert.assertNull(InfiniumVcfFields.getOptionalIntegerFromVcfOtherHeaderLine(header, "nothing"));

src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java

@@ -343,7 +343,7 @@ private void runStandardTest(final int[] lanes, final String jobName, final Stri
                             final MetricsFile<BarcodeMetric, Integer> metrics = new MetricsFile<>();
                             metrics.read(new FileReader(metricsFile));
                             Assert.assertEquals(metrics.getMetrics().get(3).PERFECT_MATCHES, expectedPfMatches);
-                            Assert.assertEquals(metrics.getMetrics().get(3).PCT_MATCHES, expectedPctMatches.doubleValue());
+                            Assert.assertEquals(metrics.getMetrics().get(3).PCT_MATCHES, expectedPctMatches);
                         }
                     }
                 }

src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java

@@ -312,7 +312,7 @@ private void runStandardTest(final int[] lanes, final String jobName, final Stri
                         final MetricsFile<BarcodeMetric, Integer> metrics = new MetricsFile<>();
                         metrics.read(new FileReader(metricsFile));
                         Assert.assertEquals(metrics.getMetrics().get(3).PERFECT_MATCHES, expectedPfMatches);
-                        Assert.assertEquals(metrics.getMetrics().get(3).PCT_MATCHES, expectedPctMatches.doubleValue());
+                        Assert.assertEquals(metrics.getMetrics().get(3).PCT_MATCHES, expectedPctMatches);
                     }
                 } finally {
                     IOUtil.recursiveDelete(outputDir);

src/test/java/picard/metrics/CollectRrbsMetricsTest.java

@@ -66,11 +66,11 @@ public void chrMReads() throws Exception {
         Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
         Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
         Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
-        Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED.doubleValue(), 0.733333);
+        Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
         Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
         Assert.assertEquals(metrics.CPG_BASES_CONVERTED.intValue(), 1);
-        Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED.doubleValue(), 0.2);
-        Assert.assertEquals(metrics.MEAN_CPG_COVERAGE.doubleValue(), 1.666667);
+        Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED, 0.2);
+        Assert.assertEquals(metrics.MEAN_CPG_COVERAGE, 1.666667);
         Assert.assertEquals(metrics.MEDIAN_CPG_COVERAGE.intValue(), 2);
         Assert.assertEquals(metrics.READS_WITH_NO_CPG.intValue(), 1);
         Assert.assertEquals(metrics.READS_IGNORED_SHORT.intValue(), 1);

src/test/java/picard/sam/DuplicationMetricsTest.java

@@ -63,7 +63,7 @@ private DuplicationMetrics nonEmptyMetrics(final int scale) {
 
     @Test
     public void testEmptyDuplicationMetricsDerivation(){
-        Assert.assertEquals(emptyMetrics().PERCENT_DUPLICATION.doubleValue(), 0.0);
+        Assert.assertEquals(emptyMetrics().PERCENT_DUPLICATION, 0.0);
     }
 
     @Test(dataProvider="testMergeDataProvider")