WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test.

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

@@ -304,7 +304,7 @@ public class LocusIteratorByState extends LocusIterator {
                     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
+                    int readOffset = state.getReadOffset();                         // the base offset on this read
 
                     final boolean isBeforeDeletion  = nextOp == CigarOperator.DELETION;
                     final boolean isAfterDeletion   = lastOp == CigarOperator.DELETION;
@@ -331,6 +331,9 @@ public class LocusIteratorByState extends LocusIterator {
                             String insertedBaseString = null;
                             if (nextOp == CigarOperator.I) {
                                 final int insertionOffset = isSingleElementCigar ? 0 : 1;
+                                // TODO -- someone please implement a better fix for the single element insertion CIGAR!
+                                if (isSingleElementCigar)
+                                    readOffset -= (nextElement.getLength() - 1); // LIBS has passed over the insertion bases!
                                 insertedBaseString = new String(Arrays.copyOfRange(read.getReadBases(), readOffset + insertionOffset, readOffset + insertionOffset + nextElement.getLength()));
                             }
 

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

@@ -208,19 +208,18 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
     }
 
     /**
-     * Test to make sure that reads supporting only an indel (example cigar string: 76I) do
+     * Test to make sure that reads supporting only an indel (example cigar string: 76I) are represented properly
-     * not negatively influence the ordering of the pileup.
      */
     @Test
-    public void testWholeIndelReadTest2() {
+    public void testWholeIndelReadRepresentedTest() {
         final int firstLocus = 44367788, secondLocus = firstLocus + 1;
 
-        SAMRecord read = ArtificialSAMUtils.createArtificialRead(header,"read",0,secondLocus,1);
+        SAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,secondLocus,1);
-        read.setReadBases(Utils.dupBytes((byte) 'A', 1));
+        read1.setReadBases(Utils.dupBytes((byte) 'A', 1));
-        read.setBaseQualities(Utils.dupBytes((byte) '@', 1));
+        read1.setBaseQualities(Utils.dupBytes((byte) '@', 1));
-        read.setCigarString("1I");
+        read1.setCigarString("1I");
 
-        List<SAMRecord> reads = Arrays.asList(read);
+        List<SAMRecord> reads = Arrays.asList(read1);
 
         // create the iterator by state with the fake reads and fake records
         li = makeLTBS(reads, createTestReadProperties());
@@ -234,6 +233,26 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
             Assert.assertFalse(pe.isAfterInsertion());
             Assert.assertEquals(pe.getEventBases(), "A");
         }
+
+        SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,secondLocus,10);
+        read2.setReadBases(Utils.dupBytes((byte) 'A', 10));
+        read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
+        read2.setCigarString("10I");
+
+        reads = Arrays.asList(read2);
+
+        // 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(), "AAAAAAAAAA");
+        }
     }
 
     private static ReadProperties createTestReadProperties() {