Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.

The problem ultimately was that ReadUtils.readStartsWithInsertion() ignores leading hard/softclips, but
ReduceReads does not.  So I refactored that method to include a boolean argument as to whether or not
clips should be ignored.  Also rebased so that return type is no longer a Pair.
Added unit test to cover this situation.

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java

@@ -207,7 +207,7 @@ public class HeaderElement {
     public void removeInsertionToTheRight() {
         this.insertionsToTheRight--;
         if (insertionsToTheRight < 0)
-            throw new ReviewedStingException("Removed too many insertions, header is now negative!");
+            throw new ReviewedStingException("Removed too many insertions, header is now negative at position " + location);
     }
 
     public boolean hasInsertionToTheRight() {

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

@@ -1199,7 +1199,7 @@ public class SlidingWindow {
         }
 
         // Special case for leading insertions before the beginning of the sliding read
-        if ( ReadUtils.readStartsWithInsertion(read).getFirst() && (readStart == headerStart || headerStart < 0) ) {
+        if ( (readStart == headerStart || headerStart < 0) && ReadUtils.readStartsWithInsertion(read.getCigar(), false) != null ) {
             // create a new first element to the window header with no bases added
             header.addFirst(new HeaderElement(readStart - 1));
             // this allows the first element (I) to look at locationIndex - 1 when we update the header and do the right thing

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

@@ -89,6 +89,25 @@ public class SlidingWindowUnitTest extends BaseTest {
         return variantRegionBitset;
     }
 
+    //////////////////////////////////////////////////////////////////////////////////////
+    //// Test for leading softclips immediately followed by an insertion in the CIGAR ////
+    //////////////////////////////////////////////////////////////////////////////////////
+
+    @Test(enabled = true)
+    public void testLeadingClipThenInsertion() {
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 10);
+        read.setReadBases(Utils.dupBytes((byte) 'A', 10));
+        read.setBaseQualities(Utils.dupBytes((byte)30, 10));
+        read.setMappingQuality(30);
+        read.setCigarString("2S2I6M");
+
+        final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 1);
+        slidingWindow.addRead(read);
+        Pair<ObjectSet<GATKSAMRecord>, CompressionStash> result = slidingWindow.close(null);
+
+    }
+
     //////////////////////////////////////////////////////////////////////////////////////
     //// This section tests the findVariantRegions() method and related functionality ////
     //////////////////////////////////////////////////////////////////////////////////////

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

@@ -424,9 +424,9 @@ public class ReadUtils {
         // clipping the left tail and first base is insertion, go to the next read coordinate
         // with the same reference coordinate. Advance to the next cigar element, or to the
         // end of the read if there is no next element.
-        Pair<Boolean, CigarElement> firstElementIsInsertion = readStartsWithInsertion(cigar);
+        final CigarElement firstElementIsInsertion = readStartsWithInsertion(cigar);
-        if (readCoord == 0 && tail == ClippingTail.LEFT_TAIL && firstElementIsInsertion.getFirst())
+        if (readCoord == 0 && tail == ClippingTail.LEFT_TAIL && firstElementIsInsertion != null)
-            readCoord = Math.min(firstElementIsInsertion.getSecond().getLength(), cigar.getReadLength() - 1);
+            readCoord = Math.min(firstElementIsInsertion.getLength(), cigar.getReadLength() - 1);
 
         return readCoord;
     }
@@ -595,25 +595,28 @@ public class ReadUtils {
     }
 
     /**
-     * Checks if a read starts with an insertion. It looks beyond Hard and Soft clips
+     * @see #readStartsWithInsertion(net.sf.samtools.Cigar, boolean) with ignoreClipOps set to true
-     * if there are any.
-     *
-     * @param read
-     * @return A pair with the answer (true/false) and the element or null if it doesn't exist
      */
-    public static Pair<Boolean, CigarElement> readStartsWithInsertion(GATKSAMRecord read) {
+    public static CigarElement readStartsWithInsertion(final Cigar cigarForRead) {
-        return readStartsWithInsertion(read.getCigar());
+        return readStartsWithInsertion(cigarForRead, true);
     }
 
-    public static Pair<Boolean, CigarElement> readStartsWithInsertion(final Cigar cigar) {
+    /**
-        for (CigarElement cigarElement : cigar.getCigarElements()) {
+     * Checks if a read starts with an insertion.
+     *
+     * @param cigarForRead    the CIGAR to evaluate
+     * @param ignoreClipOps   should we ignore S and H operators when evaluating whether an I operator is at the beginning?
+     * @return the element if it's a leading insertion or null otherwise
+     */
+    public static CigarElement readStartsWithInsertion(final Cigar cigarForRead, final boolean ignoreClipOps) {
+        for ( final CigarElement cigarElement : cigarForRead.getCigarElements() ) {
             if ( cigarElement.getOperator() == CigarOperator.INSERTION )
-                return new Pair<Boolean, CigarElement>(true, cigarElement);
+                return cigarElement;
 
-            else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP)
+            else if ( !ignoreClipOps || (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP) )
                 break;
         }
-        return new Pair<Boolean, CigarElement>(false, null);
+        return null;
     }
 
     /**