Fixing merge conflict

public/java/src/org/broadinstitute/sting/utils/MathUtils.java

@@ -408,12 +408,12 @@ public class MathUtils {
         return Math.sqrt(rms);
     }
 
-    public static double rms(Collection<Double> l) {
+    public static double rms(Collection<Integer> l) {
         if (l.size() == 0)
             return 0.0;
 
         double rms = 0.0;
-        for (Double i : l)
+        for (int i : l)
             rms += i*i;
         rms /= l.size();
         return Math.sqrt(rms);

public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

@@ -198,13 +198,15 @@ public class AlignmentUtils {
         return sum;
     }
 
-    /** Returns the mismatches in the read within the given reference context.
+    /** Returns the number of mismatches in the pileup element within the given reference context.
      *
      * @param read          the SAMRecord
      * @param ref           the reference context
-     * @return each base is represented by a bit in the BitSet. True for mismatch, false for ref
+     * @param maxMismatches the maximum number of surrounding mismatches we tolerate to consider a base good
+     * @param windowSize    window size (on each side) to test
+     * @return a bitset representing which bases are good
      */
-    public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref) {
+    public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref, int maxMismatches, int windowSize) {
         // first determine the positions with mismatches
         int readLength = read.getReadLength();
         BitSet mismatches = new BitSet(readLength);
@@ -212,7 +214,7 @@ public class AlignmentUtils {
         // it's possible we aren't starting at the beginning of a read,
         //  and we don't need to look at any of the previous context outside our window
         //  (although we do need future context)
-        int readStartPos = read.getAlignmentStart();
+        int readStartPos = Math.max(read.getAlignmentStart(), ref.getLocus().getStart() - windowSize);
         int currentReadPos = read.getAlignmentStart();
 
         byte[] refBases = ref.getBases();
@@ -263,22 +265,9 @@ public class AlignmentUtils {
                     break;
             }
         }
-        return mismatches;
-    }
-    /** Returns a BitSet showing what bases are good according to the criteria of maxMismatches in the window
-     *
-     * @param read          the SAMRecord
-     * @param ref           the reference context
-     * @param maxMismatches the maximum number of surrounding mismatches we tolerate to consider a base good
-     * @param windowSize    window size (on each side) to test
-     * @return a bitset representing which bases are good
-     */
-    public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref, int maxMismatches, int windowSize) {
-        int readLength = read.getReadLength();
 
         // all bits are set to false by default
         BitSet result = new BitSet(readLength);
-        BitSet mismatches = mismatchesInRefWindow(read, ref);
 
         int currentPos = 0, leftPos = 0, rightPos;
         int mismatchCount = 0;

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -43,6 +43,7 @@ import java.util.Map;
  *
  */
 public class GATKSAMRecord extends BAMRecord {
+    public static final String REDUCED_READ_QUALITY_TAG = "RR";
     // the SAMRecord data we're caching
     private String mReadString = null;
     private GATKSAMReadGroupRecord mReadGroup = null;
@@ -151,7 +152,7 @@ public class GATKSAMRecord extends BAMRecord {
 
     public byte[] getReducedReadCounts() {
         if ( ! retrievedReduceReadCounts ) {
-            reducedReadCounts = getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
+            reducedReadCounts = getByteArrayAttribute(REDUCED_READ_QUALITY_TAG);
             retrievedReduceReadCounts = true;
         }
 

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -51,8 +51,6 @@ public class ReadUtils {
     //
     // ----------------------------------------------------------------------------------------------------
 
-    public static final String REDUCED_READ_QUALITY_TAG = "RQ";
-
     // ----------------------------------------------------------------------------------------------------
     //
     // General utilities

public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java

@@ -29,7 +29,7 @@ public class ReadUtilsUnitTest extends BaseTest {
         reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
         reducedRead.setReadBases(BASES.getBytes());
         reducedRead.setBaseQualityString(QUALS);
-        reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
+        reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
     }
 
     private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {