Update SamComparisonMetric.java and SamComparison.java to refactor in…

…ts to longs (#1985)

* Update SamComparisonMetric.java to refactor ints to longs

This commit changes integers to longs to prevent possible overflowing of counters in cases such as the forum topic below.

https://gatk.broadinstitute.org/hc/en-us/community/posts/31913243796891-Negative-number-in-the-output-file-of-CompareSAMs

src/main/java/picard/sam/SamComparisonMetric.java

@@ -28,37 +28,37 @@ public class SamComparisonMetric extends MetricBase {
      * all records which are mapped in both files with mapping quality at most equal to LOW_MQ_THRESHOLD are counted as matching. If
      * running with LENIENT_255_MQ_ALIGNMENT=true, all records which are mapped in both files with mapping quality 255 are counted as matches.
      */
-    public int MAPPINGS_MATCH;
+    public long MAPPINGS_MATCH;
 
     /**
      * The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
      */
-    public int MAPPINGS_DIFFER;
+    public long MAPPINGS_DIFFER;
 
     /**
      * The number of primary records which are not mapped in either file.
      */
-    public int UNMAPPED_BOTH;
+    public long UNMAPPED_BOTH;
 
     /**
      * The number of primary records which are mapped in right file and found but not mapped in left file
      */
-    public int UNMAPPED_LEFT;
+    public long UNMAPPED_LEFT;
 
     /**
      * The number of primary records which are mapped in left file and found but not mapped in right file
      */
-    public int UNMAPPED_RIGHT;
+    public long UNMAPPED_RIGHT;
 
     /**
      * The number of primary records which are found in right file but not found in left file
      */
-    public int MISSING_LEFT;
+    public long MISSING_LEFT;
 
     /**
      * The number of primary records which are found in left file but not found in right file
      */
-    public int MISSING_RIGHT;
+    public long MISSING_RIGHT;
 
     /**
      * The number of primary records for which duplicate markings are different.  If running in strict duplicate
@@ -68,7 +68,7 @@ public class SamComparisonMetric extends MetricBase {
      * metric is counted on a per read basis, so a paired end fragment which differs in duplicate marking between the two
      * files will increment this metric by 2.
      */
-    public int DUPLICATE_MARKINGS_DIFFER;
+    public long DUPLICATE_MARKINGS_DIFFER;
 
     /**
      * Whether or not to consider the two input files equal.  The two input files are considered equal iff

src/main/java/picard/sam/util/SamComparison.java

@@ -374,8 +374,8 @@ private void consumeAll(
         }
     }
 
-    private int countRemaining(final SecondaryOrSupplementarySkippingIterator it) {
-        int i;
+    private long countRemaining(final SecondaryOrSupplementarySkippingIterator it) {
+        long i;
         for (i = 0; it.hasCurrent(); ++i) {
             it.advance();
         }
@@ -580,35 +580,35 @@ private static void reportDifference(Object o1, Object o2, final String label) {
         reportDifference(o1.toString(), o2.toString(), label);
     }
 
-    public int getMappingsMatch() {
+    public long getMappingsMatch() {
         return comparisonMetric.MAPPINGS_MATCH;
     }
 
-    public int getUnmappedBoth() {
+    public long getUnmappedBoth() {
         return comparisonMetric.UNMAPPED_BOTH;
     }
 
-    public int getUnmappedLeft() {
+    public long getUnmappedLeft() {
         return comparisonMetric.UNMAPPED_LEFT;
     }
 
-    public int getUnmappedRight() {
+    public long getUnmappedRight() {
         return comparisonMetric.UNMAPPED_RIGHT;
     }
 
-    public int getMappingsDiffer() {
+    public long getMappingsDiffer() {
         return comparisonMetric.MAPPINGS_DIFFER;
     }
 
-    public int getMissingLeft() {
+    public long getMissingLeft() {
         return comparisonMetric.MISSING_LEFT;
     }
 
-    public int getMissingRight() {
+    public long getMissingRight() {
         return comparisonMetric.MISSING_RIGHT;
     }
 
-    public int getDuplicateMarkingsDiffer() {
+    public long getDuplicateMarkingsDiffer() {
         return comparisonMetric.DUPLICATE_MARKINGS_DIFFER;
     }
 

src/test/java/picard/sam/util/SamComparisonTest.java

@@ -80,14 +80,14 @@ public void testSamComparison(
             final String f2,
             final boolean lenientDup,
             final boolean lenientLowMQAlignment,
-            final int expectedMatch,
-            final int expectedDiffer,
-            final int expectedUnmappedBoth,
-            final int expectedUnmappedLeft,
-            final int expectedUnmappedRight,
-            final int expectedMissingLeft,
-            final int expectedMissingRight,
-            final int expectedDupDiffer,
+            final long expectedMatch,
+            final long expectedDiffer,
+            final long expectedUnmappedBoth,
+            final long expectedUnmappedLeft,
+            final long expectedUnmappedRight,
+            final long expectedMissingLeft,
+            final long expectedMissingRight,
+            final long expectedDupDiffer,
             final boolean areEqual) throws IOException
     {
         // compare forward
@@ -114,14 +114,14 @@ private void testHelper(
             final String f2,
             final boolean lenientDup,
             final boolean lenientLowMQAlignment,
-            final int expectedMatch,
-            final int expectedDiffer,
-            final int expectedUnmappedBoth,
-            final int expectedUnmappedLeft,
-            final int expectedUnmappedRight,
-            final int expectedMissingLeft,
-            final int expectedMissingRight,
-            final int expectedDupDiffer,
+            final long expectedMatch,
+            final long expectedDiffer,
+            final long expectedUnmappedBoth,
+            final long expectedUnmappedLeft,
+            final long expectedUnmappedRight,
+            final long expectedMissingLeft,
+            final long expectedMissingRight,
+            final long expectedDupDiffer,
             final boolean areEqual) throws IOException
     {
         try (final SamReader samReader1 = SamReaderFactory.makeDefault().open(new File(TEST_FILES_DIR, f1));