BQSR with indels integrated!

* added support to base before deletion in the pileup
   * refactored covariates to operate on mismatches, insertions and deletions at the same time
   * all code is in private so original BQSR is still working as usual in public
   * outputs a molten CSV with mismatches, insertions and deletions, time to play!
   * barely tested, passes my very simple tests... haven't tested edge cases.

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

@@ -470,7 +470,7 @@ public class LocusIteratorByState extends LocusIterator {
 
                         if (op == CigarOperator.D) {
                             if (readInfo.includeReadsWithDeletionAtLoci()) {          // only add deletions to the pileup if we are authorized to do so
-                                pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
+                                pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                                 nDeletions++;
                                 if (read.getMappingQuality() == 0)
@@ -479,7 +479,7 @@ public class LocusIteratorByState extends LocusIterator {
                         }
                         else {
                             if (!filterBaseInRead(read, location.getStart())) {
-                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
+                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.D, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                                 if (read.getMappingQuality() == 0)
                                     nMQ0Reads++;

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -39,7 +39,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
 
@@ -212,7 +215,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
 
     public class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
-            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
+            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
         }
 
         @Override

public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java

@@ -87,7 +87,7 @@ public enum NGSPlatform {
     /**
      * Returns the NGSPlatform corresponding to the PL tag in the read group
      * @param plFromRG -- the PL field (or equivalent) in a ReadGroup object
-     * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match
+     * @return an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match
      */
     public static final NGSPlatform fromReadGroupPL(final String plFromRG) {
         if ( plFromRG == null ) return UNKNOWN;
@@ -105,4 +105,14 @@ public enum NGSPlatform {
 
         return UNKNOWN;
     }
+
+    /**
+     * checks whether or not the requested platform is listed in the set (and is not unknown)
+     *
+     * @param platform the read group string that describes the platform used
+     * @return true if the platform is known (i.e. it's in the list and is not UNKNOWN)
+     */
+    public static final boolean isKnown (final String platform) {
+        return fromReadGroupPL(platform) != UNKNOWN;
+    }
 }

public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -177,7 +177,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
         for (int i = 0; i < reads.size(); i++) {
             GATKSAMRecord read = reads.get(i);
             int offset = offsets.get(i);
-            pileup.add(createNewPileupElement(read, offset, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
+            pileup.add(createNewPileupElement(read, offset, false, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
         }
 
         return pileup;
@@ -196,7 +196,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
 
         UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
         for (GATKSAMRecord read : reads) {
-            pileup.add(createNewPileupElement(read, offset, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
+            pileup.add(createNewPileupElement(read, offset, false, false, false, false)); // only used to create fake pileups for testing so ancillary information is not important
         }
 
         return pileup;
@@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
 
     protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
 
-    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
+    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
 
     // --------------------------------------------------------
     //

public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java

@@ -48,7 +48,7 @@ public class ExtendedEventPileupElement extends PileupElement {
 
 
     public ExtendedEventPileupElement(GATKSAMRecord read, int offset, int eventLength, String eventBases, Type type) {
-        super(read, offset, type == Type.DELETION, false, false); // extended events are slated for removal
+        super(read, offset, type == Type.DELETION, false, false, false); // extended events are slated for removal
         this.read = read;
         this.offset = offset;
         this.eventLength = eventLength;

public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java

@@ -24,6 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
     protected final GATKSAMRecord read;
     protected final int offset;
     protected final boolean isDeletion;
+    protected final boolean isBeforeDeletion;
     protected final boolean isBeforeInsertion;
     protected final boolean isNextToSoftClip;
 
@@ -33,6 +34,7 @@ public class PileupElement implements Comparable<PileupElement> {
      * @param read              the read we are adding to the pileup
      * @param offset            the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
      * @param isDeletion        whether or not this base is a deletion
+     * @param isBeforeDeletion  whether or not this base is before a deletion
      * @param isBeforeInsertion whether or not this base is before an insertion
      * @param isNextToSoftClip  whether or not this base is next to a soft clipped base
      */
@@ -40,13 +42,14 @@ public class PileupElement implements Comparable<PileupElement> {
             "read != null",
             "offset >= -1",
             "offset <= read.getReadLength()"})
-    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
+    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
         if (offset < 0 && isDeletion)
             throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
 
         this.read = read;
         this.offset = offset;
         this.isDeletion = isDeletion;
+        this.isBeforeDeletion = isBeforeDeletion;
         this.isBeforeInsertion = isBeforeInsertion;
         this.isNextToSoftClip = isNextToSoftClip;
     }
@@ -55,6 +58,10 @@ public class PileupElement implements Comparable<PileupElement> {
         return isDeletion;
     }
 
+    public boolean isBeforeDeletion() {
+        return isBeforeDeletion;
+    }
+
     public boolean isBeforeInsertion() {
         return isBeforeInsertion;
     }

public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java

@@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
     }
 
     @Override
-    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
+    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
         throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
     }
 

public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java

@@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
     }
 
     @Override
-    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
+    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
-        return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
+        return new PileupElement(read, offset, isDeletion, isBeforeDeletion, isBeforeInsertion, isNextToSoftClip);
     }
 }

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

@@ -361,10 +361,10 @@ public class ArtificialSAMUtils {
             final GATKSAMRecord left = pair.get(0);
             final GATKSAMRecord right = pair.get(1);
 
-            pileupElements.add(new PileupElement(left, pos - leftStart, false, false, false));
+            pileupElements.add(new PileupElement(left, pos - leftStart, false, false, false, false));
 
             if (pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd()) {
-                pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false));
+                pileupElements.add(new PileupElement(right, pos - rightStart, false, false, false, false));
             }
         }
 

public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java

@@ -42,8 +42,8 @@ public class GATKSAMRecordUnitTest extends BaseTest {
 
     @Test
     public void testReducedReadPileupElement() {
-        PileupElement readp = new PileupElement(read, 0, false, false, false);
+        PileupElement readp = new PileupElement(read, 0, false, false, false, false);
-        PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false);
+        PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false, false);
 
         Assert.assertFalse(readp.getRead().isReducedRead());