Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper

* New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches.
    * Added functionality to clipping op to revert all soft clip bases in a read into matches
    * Added revertSoftClipBases function to the ReadClipper for public use
    * Wrote systematic unit tests

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

@@ -104,6 +104,10 @@ public class ClippingOp {
 
                 break;
 
+            case REVERT_SOFTCLIPPED_BASES:
+                read = revertSoftClippedBases(read);
+                break;
+
             default:
                 throw new IllegalStateException("Unexpected Clipping operator type " + algorithm);
         }
@@ -111,6 +115,38 @@ public class ClippingOp {
         return read;
     }
 
+    private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
+        GATKSAMRecord unclipped;
+
+        // shallow copy of the read bases and quals should be fine here because they are immutable in the original read
+        try {
+            unclipped = (GATKSAMRecord) read.clone();
+        } catch (CloneNotSupportedException e) {
+            throw new ReviewedStingException("Where did the clone go?");
+        }
+
+        Cigar unclippedCigar = new Cigar();
+        int matchesCount = 0;
+        for (CigarElement element : read.getCigar().getCigarElements()) {
+            if (element.getOperator() == CigarOperator.SOFT_CLIP || element.getOperator() == CigarOperator.MATCH_OR_MISMATCH)
+                matchesCount += element.getLength();
+            else if (matchesCount > 0) {
+                unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
+                matchesCount = 0;
+                unclippedCigar.add(element);
+            }
+            else
+                unclippedCigar.add(element);
+        }
+        if (matchesCount > 0)
+            unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
+
+        unclipped.setCigar(unclippedCigar);
+        unclipped.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), unclippedCigar));
+
+        return unclipped;
+    }
+
     /**
      * Given a cigar string, get the number of bases hard or soft clipped at the start
      */
@@ -472,7 +508,7 @@ public class ClippingOp {
 
         for (CigarElement cigarElement : oldCigar.getCigarElements()) {
             if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
-                oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
+                oldShift += cigarElement.getLength();
             else if (readHasStarted)
                 break;
         }

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

@@ -29,5 +29,10 @@ public enum ClippingRepresentation {
      * lossy) operation.  Note that this can only be applied to cases where the clipped
      * bases occur at the start or end of a read.
      */
-    HARDCLIP_BASES
+    HARDCLIP_BASES,
+
+    /**
+     * Turn all soft-clipped bases into matches
+     */
+    REVERT_SOFTCLIPPED_BASES,
 }

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

@@ -213,4 +213,9 @@ public class ReadClipper {
         }
         return clipRead(ClippingRepresentation.HARDCLIP_BASES);
     }
+
+    public GATKSAMRecord revertSoftClippedBases() {
+        this.addOp(new ClippingOp(0, 0));     // UNSOFTCLIP_BASES doesn't need coordinates
+        return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
+    }
 }

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

@@ -279,9 +279,9 @@ public class ReadClipperUnitTest extends BaseTest {
                 GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
                 GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
 
-                int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
+                int expectedLength = read.getReadLength() - leadingCigarElementLength(read.getCigar(), CigarOperator.INSERTION);
                 if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
-                    expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
+                    expectedLength -= leadingCigarElementLength(ReadClipperTestUtils.invertCigar(read.getCigar()), CigarOperator.INSERTION);
 
                 if (! clippedRead.isEmpty()) {
                     Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString()));  // check that everything else is still there
@@ -293,6 +293,27 @@ public class ReadClipperUnitTest extends BaseTest {
         }
     }
 
+    @Test(enabled = true)
+    public void testRevertSoftClippedBases()
+    {
+        for (Cigar cigar:  cigarList) {
+            final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
+            final int tailSoftClips = leadingCigarElementLength(ReadClipperTestUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
+
+            final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
+            final GATKSAMRecord unclipped = (new ReadClipper(read)).revertSoftClippedBases();
+
+            if ( leadingSoftClips > 0 || tailSoftClips > 0) {
+                final int expectedStart = read.getAlignmentStart() - leadingSoftClips;
+                final int expectedEnd = read.getAlignmentEnd() + tailSoftClips;
+
+                Assert.assertEquals(unclipped.getAlignmentStart(), expectedStart);
+                Assert.assertEquals(unclipped.getAlignmentEnd(), expectedEnd);
+            }
+            else
+                Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
+        }
+    }
 
 
     private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {
@@ -304,12 +325,12 @@ public class ReadClipperUnitTest extends BaseTest {
     }
 
     private boolean startsWithInsertion(Cigar cigar) {
-        return leadingInsertionLength(cigar) > 0;
+        return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
     }
 
-    private int leadingInsertionLength(Cigar cigar) {
+    private int leadingCigarElementLength(Cigar cigar, CigarOperator operator) {
         for (CigarElement cigarElement : cigar.getCigarElements()) {
-            if (cigarElement.getOperator() == CigarOperator.INSERTION)
+            if (cigarElement.getOperator() == operator)
                 return cigarElement.getLength();
             if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
                 break;