Bugfix for ReadClipper with ReducedReads

-- The previous version of the read clipping operations wouldn't modify the reduced reads counts, so hardClipToRegion would result in a read with, say, 50 bp of sequence and base qualities but 250 bp of reduced read counts.  Updated the hardClip operation to handle reduce reads, and added a unit test to make sure this works properly.  Also had to update GATKSAMRecord.emptyRead() to set the reduced count to new byte[0] if the template read is a reduced read
-- Update md5s, where the new code recovers a TP variant with count 2 that was missed previously

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("3c87eb93ffe3a0166aca753050b981e1"));
+                Arrays.asList("0df626cd0d76aca8a05a545d0b36bf23"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
 

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

@@ -378,7 +378,13 @@ public class ClippingOp {
             hardClippedRead.setBaseQualities(newBaseInsertionQuals, EventType.BASE_INSERTION);
             hardClippedRead.setBaseQualities(newBaseDeletionQuals, EventType.BASE_DELETION);
         }
-        
+
+        if (read.isReducedRead()) {
+            final byte[] reducedCounts = new byte[newLength];
+            System.arraycopy(read.getReducedReadCounts(), copyStart, reducedCounts, 0, newLength);
+            hardClippedRead.setReducedReadCounts(reducedCounts);
+        }
+
         return hardClippedRead;
 
     }

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -393,6 +393,22 @@ public class GATKSAMRecord extends BAMRecord {
         setAttribute(REDUCED_READ_CONSENSUS_TAG, counts);
     }
 
+    /**
+     * Set the reduced read counts tag for this record to counts
+     *
+     * Note that this function does not set the REDUCED_READ_CONSENSUS_TAG value, it's purely for manipulating
+     * the underlying reduced reads count
+     *
+     * TODO -- this function needs to be fixed when the RR spec is set to 2.0
+     *
+     * @param counts the count array
+     */
+    public void setReducedReadCounts(final byte[] counts) {
+        if ( counts.length != getReadBases().length ) throw new IllegalArgumentException("Reduced counts length " + counts.length + " != bases length " + getReadBases().length);
+        retrievedReduceReadCounts = true;
+        reducedReadCounts = counts;
+    }
+
     /**
      * The number of bases corresponding the i'th base of the reduced read.
      *
@@ -678,6 +694,7 @@ public class GATKSAMRecord extends BAMRecord {
         emptyRead.setCigarString("");
         emptyRead.setReadBases(new byte[0]);
         emptyRead.setBaseQualities(new byte[0]);
+        if ( read.isReducedRead() ) emptyRead.setReducedReadCounts(new byte[0]);
 
         SAMReadGroupRecord samRG = read.getReadGroup();
         emptyRead.clearAttributes();

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

@@ -35,6 +35,7 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 
@@ -348,4 +349,20 @@ public class ReadClipperUnitTest extends BaseTest {
 
     }
 
+    @Test(enabled = true)
+    public void testHardClipReducedRead() {
+        GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar("10M");
+        final byte[] counts = new byte[read.getReadLength()];
+        for ( int i = 0; i < counts.length; i++ ) counts[i] = (byte)i;
+        read.setReducedReadCounts(counts);
+        int alnStart = read.getAlignmentStart();
+        int alnEnd = read.getAlignmentEnd();
+        int readLength = read.getReadLength();
+        for (int i = 0; i < readLength / 2; i++) {
+            GATKSAMRecord clippedRead = ReadClipper.hardClipBothEndsByReferenceCoordinates(read, alnStart + i, alnEnd - i);
+            final byte[] expectedReducedCounts = Arrays.copyOfRange(counts, i + 1, readLength - i - 1);
+            Assert.assertEquals(clippedRead.getReducedReadCounts(), expectedReducedCounts);
+        }
+    }
+
 }