fixes after code review

broadinstitute · Jan 24, 2017 · 41797cf · 41797cf
1 parent 191354c
commit 41797cf
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Showing 3 changed files with 32 additions and 31 deletions.
diff --git a/src/test/java/picard/analysis/CollectJumpingLibraryMetricsTest.java b/src/test/java/picard/analysis/CollectJumpingLibraryMetricsTest.java
@@ -32,19 +32,19 @@ public void testCollectJumpingLibraryMetrics() throws IOException {
             Assert.assertEquals(metrics.JUMP_DUPLICATE_PAIRS, 1);
             Assert.assertEquals(metrics.JUMP_DUPLICATE_PCT, 0.25);
             Assert.assertEquals(metrics.JUMP_LIBRARY_SIZE, 6);
-            Assert.assertEquals((int)metrics.JUMP_MEAN_INSERT_SIZE, 176);
-            Assert.assertEquals((int)metrics.JUMP_STDEV_INSERT_SIZE, 50);
+            Assert.assertEquals(metrics.JUMP_MEAN_INSERT_SIZE, 176.0);
+            Assert.assertEquals(metrics.JUMP_STDEV_INSERT_SIZE, 50.0);
             Assert.assertEquals(metrics.NONJUMP_PAIRS, 1);
             Assert.assertEquals(metrics.NONJUMP_DUPLICATE_PAIRS, 0);
-            Assert.assertEquals((int)metrics.NONJUMP_DUPLICATE_PCT, 0);
+            Assert.assertEquals(metrics.NONJUMP_DUPLICATE_PCT, 0.0);
             Assert.assertEquals(metrics.NONJUMP_LIBRARY_SIZE, 0);
-            Assert.assertEquals((int)metrics.NONJUMP_MEAN_INSERT_SIZE, 96);
-            Assert.assertEquals((int)metrics.NONJUMP_STDEV_INSERT_SIZE, 0);
+            Assert.assertEquals(metrics.NONJUMP_MEAN_INSERT_SIZE, 96.0);
+            Assert.assertEquals(metrics.NONJUMP_STDEV_INSERT_SIZE, Double.NaN);
             Assert.assertEquals(metrics.CHIMERIC_PAIRS, 0);
             Assert.assertEquals(metrics.FRAGMENTS, 1);
             Assert.assertEquals(metrics.PCT_JUMPS, 0.8);
             Assert.assertEquals(metrics.PCT_NONJUMPS, 0.2);
-            Assert.assertEquals((int)metrics.PCT_CHIMERAS, 0);
+            Assert.assertEquals(metrics.PCT_CHIMERAS, 0.0);
         }
     }
-}
+}
diff --git a/src/test/java/picard/analysis/CollectOxoGMetricsTest.java b/src/test/java/picard/analysis/CollectOxoGMetricsTest.java
@@ -31,28 +31,29 @@ public void testCollectOxoGMetrics() throws IOException {
         final MetricsFile<CollectOxoGMetrics.CpcgMetrics, Comparable<?>> output = new MetricsFile<>();
         output.read(new FileReader(outputFile));
 
-        final CollectOxoGMetrics.CpcgMetrics cpcgMetrics = output.getMetrics().get(4);
-
-        Assert.assertEquals(cpcgMetrics.SAMPLE_ALIAS, "Hi,Momma!");
-        Assert.assertEquals(cpcgMetrics.LIBRARY, "whatever");
-        Assert.assertEquals(cpcgMetrics.CONTEXT, "TCT");
-        Assert.assertEquals(cpcgMetrics.TOTAL_SITES, 3);
-        Assert.assertEquals(cpcgMetrics.TOTAL_BASES, 3);
-        Assert.assertEquals(cpcgMetrics.REF_NONOXO_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.REF_OXO_BASES, 3);
-        Assert.assertEquals(cpcgMetrics.REF_TOTAL_BASES, 3);
-        Assert.assertEquals(cpcgMetrics.ALT_NONOXO_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.ALT_OXO_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.OXIDATION_ERROR_RATE, 0.333333);
-        Assert.assertEquals(cpcgMetrics.OXIDATION_Q, 4.771213);
-        Assert.assertEquals(cpcgMetrics.C_REF_REF_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.G_REF_REF_BASES, 3);
-        Assert.assertEquals(cpcgMetrics.C_REF_ALT_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.G_REF_ALT_BASES, 0);
-        Assert.assertEquals(cpcgMetrics.C_REF_OXO_ERROR_RATE, Double.NaN);
-        Assert.assertEquals(cpcgMetrics.C_REF_OXO_Q, Double.NaN);
-        Assert.assertEquals(cpcgMetrics.G_REF_OXO_ERROR_RATE, Double.NaN);
-        Assert.assertEquals(cpcgMetrics.G_REF_OXO_Q, Double.NaN);
+        final int metricsNumber = 4; // metrics number for testing (randomly chosen) that corresponds "TCT" context string.
+        final CollectOxoGMetrics.CpcgMetrics metrics = output.getMetrics().get(metricsNumber);
+
+        Assert.assertEquals(metrics.SAMPLE_ALIAS, "Hi,Momma!");
+        Assert.assertEquals(metrics.LIBRARY, "whatever");
+        Assert.assertEquals(metrics.CONTEXT, "TCT");
+        Assert.assertEquals(metrics.TOTAL_SITES, 3);
+        Assert.assertEquals(metrics.TOTAL_BASES, 3);
+        Assert.assertEquals(metrics.REF_NONOXO_BASES, 0);
+        Assert.assertEquals(metrics.REF_OXO_BASES, 3);
+        Assert.assertEquals(metrics.REF_TOTAL_BASES, 3);
+        Assert.assertEquals(metrics.ALT_NONOXO_BASES, 0);
+        Assert.assertEquals(metrics.ALT_OXO_BASES, 0);
+        Assert.assertEquals(metrics.OXIDATION_ERROR_RATE, 0.333333);
+        Assert.assertEquals(metrics.OXIDATION_Q, 4.771213);
+        Assert.assertEquals(metrics.C_REF_REF_BASES, 0);
+        Assert.assertEquals(metrics.G_REF_REF_BASES, 3);
+        Assert.assertEquals(metrics.C_REF_ALT_BASES, 0);
+        Assert.assertEquals(metrics.G_REF_ALT_BASES, 0);
+        Assert.assertEquals(metrics.C_REF_OXO_ERROR_RATE, Double.NaN);
+        Assert.assertEquals(metrics.C_REF_OXO_Q, Double.NaN);
+        Assert.assertEquals(metrics.G_REF_OXO_ERROR_RATE, Double.NaN);
+        Assert.assertEquals(metrics.G_REF_OXO_Q, Double.NaN);
     }
 
     @DataProvider(name = "RightOptions")
@@ -126,4 +127,4 @@ private static CollectOxoGMetrics getCollectOxoGMetrics(final int minimumInsertS
         collectOxoGMetrics.CONTEXTS = context;
         return collectOxoGMetrics;
     }
-}
+}
diff --git a/src/test/java/picard/fastq/BamToBfqTest.java b/src/test/java/picard/fastq/BamToBfqTest.java
@@ -45,4 +45,4 @@ public void testBamToBfq(final File input, final boolean isPairedRun,
             TestUtil.recursiveDelete(analysisDir);
         }
     }
-}
+}