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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-08-20 23:12:58 -04:00
parent 3514fb6e66 40d5efc804
commit 3dfe8df262
2 changed files with 43 additions and 11 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -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)
insertedBaseString = new String(Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + nextElement.getLength()));
if (nextOp == CigarOperator.I) {
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++;

29
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
View File

@ -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(),