Merge pull request #254 from broadinstitute/md_bad_merge

Fix error in merging code in HC

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

@@ -260,7 +260,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
     public void testDivideByZero() {
         String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s ";
         // we expect to lose coverage due to the downsampling so don't run the systematic tests
-        executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("c459a6153a17c2cbf8441e1918fda9c8")));
+        executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("4f0ef477c0417d1eb602b323474ef377")));
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
+import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
 
@@ -559,26 +560,34 @@ public class ClippingOp {
         return new CigarShift(cleanCigar, shiftFromStart, shiftFromEnd);
     }
 
+    /**
+     * Compute the offset of the first "real" position in the cigar on the genome
+     *
+     * This is defined as a first position after a run of Hs followed by a run of Ss
+     *
+     * @param cigar A non-null cigar
+     * @return the offset (from 0) of the first on-genome base
+     */
+    private int calcHardSoftOffset(final Cigar cigar) {
+        final List<CigarElement> elements = cigar.getCigarElements();
+
+        int size = 0;
+        int i = 0;
+        while ( i < elements.size() && elements.get(i).getOperator() == CigarOperator.HARD_CLIP ) {
+            size += elements.get(i).getLength();
+            i++;
+        }
+        while ( i < elements.size() && elements.get(i).getOperator() == CigarOperator.SOFT_CLIP ) {
+            size += elements.get(i).getLength();
+            i++;
+        }
+
+        return size;
+    }
+
     private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
-        int newShift = 0;
+        final int newShift = calcHardSoftOffset(newCigar);
-        int oldShift = 0;
+        final int oldShift = calcHardSoftOffset(oldCigar);
-
-        boolean readHasStarted = false;  // if the new cigar is composed of S and H only, we have to traverse the entire old cigar to calculate the shift
-        for (CigarElement cigarElement : newCigar.getCigarElements()) {
-            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
-                newShift += cigarElement.getLength();
-            else {
-                readHasStarted = true;
-                break;
-            }
-        }
-
-        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
-            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
-                oldShift += cigarElement.getLength();
-            else if (readHasStarted)
-                break;
-        }
         return newShift - oldShift;
     }
 

public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java

@@ -48,7 +48,7 @@ import java.util.List;
 public class ReadClipperUnitTest extends BaseTest {
 
     List<Cigar> cigarList;
-    int maximumCigarSize = 6;                                                                                           // 6 is the minimum necessary number to try all combinations of cigar types with guarantee of clipping an element with length = 2
+    int maximumCigarSize = 10;                                                                                           // 6 is the minimum necessary number to try all combinations of cigar types with guarantee of clipping an element with length = 2
 
     @BeforeClass
     public void init() {
@@ -391,4 +391,11 @@ public class ReadClipperUnitTest extends BaseTest {
         }
     }
 
+    @Test(enabled = true)
+    public void testRevertEntirelySoftclippedReads() {
+        GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar("2H1S3H");
+        GATKSAMRecord clippedRead = ReadClipper.revertSoftClippedBases(read);
+        Assert.assertEquals(clippedRead.getAlignmentStart(), read.getSoftStart());
+    }
+
 }