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

@@ -104,7 +104,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         after.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20});
         after.setCigarString("10M");
 
-        List<SAMRecord> reads = Arrays.asList(before,during,after);
+        List<SAMRecord> reads = Arrays.asList(before, during, after);
 
         // create the iterator by state with the fake reads and fake records
         li = makeLTBS(reads,readAttributes);
@@ -134,9 +134,9 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         // create a test version of the Reads object
         ReadProperties readAttributes = createTestReadProperties();
 
-        SAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header,"indelOnly",0,firstLocus,76);
+        SAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
         indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
-        indelOnlyRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
+        indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
         indelOnlyRead.setCigarString("76I");
 
         List<SAMRecord> reads = Arrays.asList(indelOnlyRead);
@@ -148,10 +148,10 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         // and considers it to be an indel-containing read.
         Assert.assertTrue(li.hasNext(),"Should have found a whole-indel read in the normal base pileup without extended events enabled");
         AlignmentContext alignmentContext = li.next();
-        Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Base pileup is at incorrect location.");
+        Assert.assertEquals(alignmentContext.getLocation().getStart(), firstLocus, "Base pileup is at incorrect location.");
         ReadBackedPileup basePileup = alignmentContext.getBasePileup();
         Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
-        Assert.assertSame(basePileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
+        Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
     }
 
     /**
@@ -168,7 +168,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         leadingRead.setCigarString("1M75I");
 
         SAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header,"indelOnly",0,secondLocus,76);
-        indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
+        indelOnlyRead.setReadBases(Utils.dupBytes((byte) 'A', 76));
         indelOnlyRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
         indelOnlyRead.setCigarString("76I");
 
@@ -177,7 +177,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte)'@',76));
         fullMatchAfterIndel.setCigarString("75I1M");
 
-        List<SAMRecord> reads = Arrays.asList(leadingRead,indelOnlyRead,fullMatchAfterIndel);
+        List<SAMRecord> reads = Arrays.asList(leadingRead, indelOnlyRead, fullMatchAfterIndel);
 
         // create the iterator by state with the fake reads and fake records
         li = makeLTBS(reads, createTestReadProperties());
@@ -204,7 +204,36 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
             numAlignmentContextsFound++;
         }
 
-        Assert.assertEquals(numAlignmentContextsFound,2,"Found incorrect number of alignment contexts");
+        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() {