updated new method names as per PR comments

Author: holmeso

qprofiler/src/org/qcmg/qprofiler/bam/BamSummaryReport.java

@@ -576,16 +576,16 @@ private void parseTAGs(final SAMRecord record, final MAPQMatrix matrix, final by
             }
         }
 
-        parseStringAttribute(record.getAttribute("RG"), tagRGLineLengths);
+        aggregateStringAttribute(record.getAttribute("RG"), tagRGLineLengths);
         if (!torrentBam) {
-            parseIntegerAttribute(record.getAttribute("ZM"), tagZMLineLengths, includeMatrices, matrix, MatrixType.ZM);
-            parseIntegerAttribute(record.getAttribute("ZF"), tagZFLineLengths, false, null, null);
-            parseStringAttribute(record.getAttribute("ZP"), tagZPLineLengths);
-        }
-        parseIntegerAttribute(record.getAttribute("CM"), tagCMLineLengths, includeMatrices, matrix, MatrixType.CM);
-        parseIntegerAttribute(record.getAttribute("SM"), tagSMLineLengths, includeMatrices, matrix, MatrixType.SM);
-        parseIntegerAttribute(record.getAttribute("IH"), tagIHLineLengths, false, null, null);
-        parseIntegerAttribute(record.getAttribute("NH"), tagNHLineLengths, includeMatrices, matrix, MatrixType.NH);
+            aggregateIntegerAttribute(record.getAttribute("ZM"), tagZMLineLengths, includeMatrices, matrix, MatrixType.ZM);
+            aggregateIntegerAttribute(record.getAttribute("ZF"), tagZFLineLengths, false, null, null);
+            aggregateStringAttribute(record.getAttribute("ZP"), tagZPLineLengths);
+        }
+        aggregateIntegerAttribute(record.getAttribute("CM"), tagCMLineLengths, includeMatrices, matrix, MatrixType.CM);
+        aggregateIntegerAttribute(record.getAttribute("SM"), tagSMLineLengths, includeMatrices, matrix, MatrixType.SM);
+        aggregateIntegerAttribute(record.getAttribute("IH"), tagIHLineLengths, false, null, null);
+        aggregateIntegerAttribute(record.getAttribute("NH"), tagNHLineLengths, includeMatrices, matrix, MatrixType.NH);
         //MD
         if (!includeMDTag) {
             value = (String) record.getAttribute(SAMTag.MD);
@@ -626,8 +626,8 @@ private void parseTAGs(final SAMRecord record, final MAPQMatrix matrix, final by
         }
     }
 
-    public static void parseIntegerAttribute(Object attribute,
-                                             final QCMGAtomicLongArray array, boolean includeMatrices, final MAPQMatrix matrix, MatrixType matrixType) {
+    public static void aggregateIntegerAttribute(Object attribute,
+                                                 final QCMGAtomicLongArray array, boolean includeMatrices, final MAPQMatrix matrix, MatrixType matrixType) {
         if (attribute instanceof Integer) {
             if (null != array) {
                 array.increment((Integer) attribute);
@@ -638,7 +638,7 @@ public static void parseIntegerAttribute(Object attribute,
         }
     }
 
-    public static void parseStringAttribute(Object attribute, final ConcurrentMap<String, AtomicLong> map) {
+    public static void aggregateStringAttribute(Object attribute, final ConcurrentMap<String, AtomicLong> map) {
         if (attribute instanceof String && null != map) {
             SummaryByCycleUtils.incrementCount(map, (String) attribute);
         }

qprofiler/test/org/qcmg/qprofiler/bam/BamSummaryReportTest.java

@@ -192,15 +192,15 @@ public void testGenerateMAPQSubMaps() throws Exception {
     public void parseIntegerAttribute() {
         QCMGAtomicLongArray array = new QCMGAtomicLongArray(100);
         MAPQMatrix matrix = new MAPQMatrix();
-        BamSummaryReport.parseIntegerAttribute(null, array, true, matrix, MAPQMatrix.MatrixType.ZM);
+        BamSummaryReport.aggregateIntegerAttribute(null, array, true, matrix, MAPQMatrix.MatrixType.ZM);
         assertTrue(array.isEmpty());
         assertEquals(0, matrix.getMatrixByType(MAPQMatrix.MatrixType.ZM).size());
-        BamSummaryReport.parseIntegerAttribute("hello", array, true, matrix, MAPQMatrix.MatrixType.ZM);
+        BamSummaryReport.aggregateIntegerAttribute("hello", array, true, matrix, MAPQMatrix.MatrixType.ZM);
         assertTrue(array.isEmpty());
         assertEquals(0, matrix.getMatrixByType(MAPQMatrix.MatrixType.ZM).size());
-        BamSummaryReport.parseIntegerAttribute(1, array, true, matrix, MAPQMatrix.MatrixType.ZM);
+        BamSummaryReport.aggregateIntegerAttribute(1, array, true, matrix, MAPQMatrix.MatrixType.ZM);
         assertEquals(1, array.get(1));
-        BamSummaryReport.parseIntegerAttribute(10, array, true, matrix, MAPQMatrix.MatrixType.ZM);
+        BamSummaryReport.aggregateIntegerAttribute(10, array, true, matrix, MAPQMatrix.MatrixType.ZM);
         assertEquals(1, array.get(1));
         assertEquals(1, array.get(10));
         assertEquals(2, matrix.getMatrixByType(MAPQMatrix.MatrixType.ZM).size());
@@ -212,24 +212,24 @@ public void parseStringAttributeTest() {
         ConcurrentMap<String, AtomicLong> map = new ConcurrentHashMap<>();
 
         // Scenario 1: null attribute, null map
-        BamSummaryReport.parseStringAttribute(null, null);
+        BamSummaryReport.aggregateStringAttribute(null, null);
         assertTrue(map.isEmpty());
         // Scenario 2: null attribute, null map
-        BamSummaryReport.parseStringAttribute(null, map);
+        BamSummaryReport.aggregateStringAttribute(null, map);
         assertTrue(map.isEmpty());
 
         // Scenario 3: Non-String attribute
-        BamSummaryReport.parseStringAttribute(123, map);
+        BamSummaryReport.aggregateStringAttribute(123, map);
         // Since the input parameter was not a string, no modification should have been made to the map
         assertEquals(map.size(), 0);
 
         // Scenario 4: String attribute, null map
-        BamSummaryReport.parseStringAttribute("testAttribute", null);
+        BamSummaryReport.aggregateStringAttribute("testAttribute", null);
         // Now, the map should contain an entry with key 'testAttribute' with a count of 1
         assertEquals(map.size(), 0);
 
         // Scenario 5: String attribute, null map
-        BamSummaryReport.parseStringAttribute("testAttribute", map);
+        BamSummaryReport.aggregateStringAttribute("testAttribute", map);
         assertEquals(map.size(), 1);
     }