Fix for Adam K's reported bug: we weren't handling reads that were entirely insertions properly in LIBS. Specifically, the event bases were off-by-one (which was disasterous in Adam's case with a 1bp read). Added a unit test to cover this case.

public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -301,6 +301,7 @@ public class LocusIteratorByState extends LocusIterator {
                     final CigarOperator op = state.getCurrentCigarOperator();       // current cigar operator
                     final CigarElement nextElement = state.peekForwardOnGenome();   // next cigar element
                     final CigarElement lastElement = state.peekBackwardOnGenome();  // last cigar element
+                    final boolean isSingleElementCigar = nextElement == lastElement;
                     final CigarOperator nextOp = nextElement.getOperator();         // next cigar operator
                     final CigarOperator lastOp = lastElement.getOperator();         // last cigar operator
                     final int readOffset = state.getReadOffset();                   // the base offset on this read
@@ -308,7 +309,7 @@ public class LocusIteratorByState extends LocusIterator {
                     final boolean isBeforeDeletion  = nextOp == CigarOperator.DELETION;
                     final boolean isAfterDeletion   = lastOp == CigarOperator.DELETION;
                     final boolean isBeforeInsertion = nextOp == CigarOperator.INSERTION;
-                    final boolean isAfterInsertion  = lastOp == CigarOperator.INSERTION;
+                    final boolean isAfterInsertion  = lastOp == CigarOperator.INSERTION && !isSingleElementCigar;
                     final boolean isNextToSoftClip  = nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart());
 
                     int nextElementLength = nextElement.getLength();
@@ -328,8 +329,10 @@ public class LocusIteratorByState extends LocusIterator {
                     else {
                         if (!filterBaseInRead(read, location.getStart())) {
                             String insertedBaseString = null;
-                            if (nextOp == CigarOperator.I)
+                            if (nextOp == CigarOperator.I) {
-                                insertedBaseString = new String(Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + nextElement.getLength()));
+                                final int insertionOffset = isSingleElementCigar ? 0 : 1;
+                                insertedBaseString = new String(Arrays.copyOfRange(read.getReadBases(), readOffset + insertionOffset, readOffset + insertionOffset + nextElement.getLength()));
+                            }
 
                             pile.add(new PileupElement(read, readOffset, false, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, insertedBaseString, nextElementLength));
                             size++;

public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -207,6 +207,35 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         Assert.assertEquals(numAlignmentContextsFound, 2, "Found incorrect number of alignment contexts");
     }
 
+    /**
+     * Test to make sure that reads supporting only an indel (example cigar string: 76I) do
+     * not negatively influence the ordering of the pileup.
+     */
+    @Test
+    public void testWholeIndelReadTest2() {
+        final int firstLocus = 44367788, secondLocus = firstLocus + 1;
+
+        SAMRecord read = ArtificialSAMUtils.createArtificialRead(header,"read",0,secondLocus,1);
+        read.setReadBases(Utils.dupBytes((byte) 'A', 1));
+        read.setBaseQualities(Utils.dupBytes((byte) '@', 1));
+        read.setCigarString("1I");
+
+        List<SAMRecord> reads = Arrays.asList(read);
+
+        // create the iterator by state with the fake reads and fake records
+        li = makeLTBS(reads, createTestReadProperties());
+
+        while(li.hasNext()) {
+            AlignmentContext alignmentContext = li.next();
+            ReadBackedPileup p = alignmentContext.getBasePileup();
+            Assert.assertTrue(p.getNumberOfElements() == 1);
+            PileupElement pe = p.iterator().next();
+            Assert.assertTrue(pe.isBeforeInsertion());
+            Assert.assertFalse(pe.isAfterInsertion());
+            Assert.assertEquals(pe.getEventBases(), "A");
+        }
+    }
+
     private static ReadProperties createTestReadProperties() {
         return new ReadProperties(
                 Collections.<SAMReaderID>emptyList(),