Fix error in merging code in HC

-- Ultimately this was caused by an underlying bug in the reverting of soft clipped bases in the read clipper.  The read clipper would fail to properly set the alignment start for reads that were 100% clipped before reverting, such as 10H2S5H => 10H2M5H.  This has been fixed and unit tested.
-- Update 1 ReduceReads MD5, which was due to cases where we were clipping away all of the MATCH part of the read, leaving a cigar like 50H11S and the revert soft clips was failing to properly revert the bases.
-- delivers #50655421

protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java

@@ -260,7 +260,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
     public void testDivideByZero() {
         String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s ";
         // we expect to lose coverage due to the downsampling so don't run the systematic tests
-        executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("c459a6153a17c2cbf8441e1918fda9c8")));
+        executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("4f0ef477c0417d1eb602b323474ef377")));
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
+import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
 
@@ -559,26 +560,34 @@ public class ClippingOp {
         return new CigarShift(cleanCigar, shiftFromStart, shiftFromEnd);
     }
 
+    /**
+     * Compute the offset of the first "real" position in the cigar on the genome
+     *
+     * This is defined as a first position after a run of Hs followed by a run of Ss
+     *
+     * @param cigar A non-null cigar
+     * @return the offset (from 0) of the first on-genome base
+     */
+    private int calcHardSoftOffset(final Cigar cigar) {
+        final List<CigarElement> elements = cigar.getCigarElements();
+
+        int size = 0;
+        int i = 0;
+        while ( i < elements.size() && elements.get(i).getOperator() == CigarOperator.HARD_CLIP ) {
+            size += elements.get(i).getLength();
+            i++;
+        }
+        while ( i < elements.size() && elements.get(i).getOperator() == CigarOperator.SOFT_CLIP ) {
+            size += elements.get(i).getLength();
+            i++;
+        }
+
+        return size;
+    }
+
     private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
-        int newShift = 0;
-        int oldShift = 0;
-
-        boolean readHasStarted = false;  // if the new cigar is composed of S and H only, we have to traverse the entire old cigar to calculate the shift
-        for (CigarElement cigarElement : newCigar.getCigarElements()) {
-            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
-                newShift += cigarElement.getLength();
-            else {
-                readHasStarted = true;
-                break;
-            }
-        }
-
-        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
-            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
-                oldShift += cigarElement.getLength();
-            else if (readHasStarted)
-                break;
-        }
+        final int newShift = calcHardSoftOffset(newCigar);
+        final int oldShift = calcHardSoftOffset(oldCigar);
         return newShift - oldShift;
     }
 

public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java

@@ -48,7 +48,7 @@ import java.util.List;
 public class ReadClipperUnitTest extends BaseTest {
 
     List<Cigar> cigarList;
-    int maximumCigarSize = 6;                                                                                           // 6 is the minimum necessary number to try all combinations of cigar types with guarantee of clipping an element with length = 2
+    int maximumCigarSize = 10;                                                                                           // 6 is the minimum necessary number to try all combinations of cigar types with guarantee of clipping an element with length = 2
 
     @BeforeClass
     public void init() {
@@ -391,4 +391,11 @@ public class ReadClipperUnitTest extends BaseTest {
         }
     }
 
+    @Test(enabled = true)
+    public void testRevertEntirelySoftclippedReads() {
+        GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar("2H1S3H");
+        GATKSAMRecord clippedRead = ReadClipper.revertSoftClippedBases(read);
+        Assert.assertEquals(clippedRead.getAlignmentStart(), read.getSoftStart());
+    }
+
 }