Count Reads should use a Long instead of an Integer for counts to prevent overflows. Added unit test.

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java

@@ -66,11 +66,16 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountReads extends ReadWalker<Integer, Integer> implements NanoSchedulable {
+public class CountReads extends ReadWalker<Integer, Long> implements NanoSchedulable {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
         return 1;
     }
 
-    @Override public Integer reduceInit() { return 0; }
+    @Override public Long reduceInit() { return 0L; }
-    @Override public Integer reduce(Integer value, Integer sum) { return value + sum; }
+
+    public Long reduce(Integer value, Long sum) { return (long) value + sum; }
+
+    public void onTraversalDone(Long result) {
+        logger.info("CountReads counted " + result + " reads in the traversal");
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java

@@ -153,11 +153,11 @@ public class TraverseReadsUnitTest extends BaseTest {
 
         countReadWalker.onTraversalDone(accumulator);
 
-        if (!(accumulator instanceof Integer)) {
+        if (!(accumulator instanceof Long)) {
-            fail("Count read walker should return an interger.");
+            fail("Count read walker should return a Long.");
         }
-        if (((Integer) accumulator) != 10000) {
+        if (!accumulator.equals(new Long(10000))) {
-            fail("there should be 10000 mapped reads in the index file, there was " + ((Integer) accumulator));
+            fail("there should be 10000 mapped reads in the index file, there was " + (accumulator));
         }
     }
 

public/java/test/org/broadinstitute/sting/gatk/walkers/qc/CountReadsUnitTest.java

@@ -0,0 +1,49 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class CountReadsUnitTest {
+
+    @Test
+    public void testReadsDoNotOverflowInt() {
+
+        final CountReads walker = new CountReads();
+
+        final long moreThanMaxInt = ((long)Integer.MAX_VALUE) + 1L;
+
+        Long sum = walker.reduceInit();
+
+        for ( long i = 0L; i < moreThanMaxInt; i++ ) {
+            final Integer x = walker.map(null, null, null);
+            sum = walker.reduce(x, sum);
+        }
+
+        Assert.assertEquals(sum.longValue(), moreThanMaxInt);
+    }
+}