From c2e27729c79801afdcfd5e070e4bc5309f75b370 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 29 Mar 2012 17:08:25 -0400
Subject: [PATCH] Renaming PileupElement.isBeforeDeletion() to
 PileupElement.isBeforeDeletedBase() so that it's more clear that it can still
 be true while inside a deletion.  Added PileupElement.isBeforeDeletionStart()
 to cover the case that I want where we only trigger before the actual
 deletion event.  Similarly for after a deletion.  Updated counting code in
 ConsensusAlleleCounter accordingly.

---
 .../genotyper/ConsensusAlleleCounter.java     |  2 +-
 ...NPGenotypeLikelihoodsCalculationModel.java |  2 +-
 .../pileup/AbstractReadBackedPileup.java      |  6 ++---
 .../sting/utils/pileup/PileupElement.java     | 24 ++++++++++++-------
 4 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index 2999c5249..c25517927 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -216,7 +216,7 @@ public class ConsensusAlleleCounter {
                     }
 
                 }
-                else if ( p.isBeforeDeletion() ) {
+                else if ( p.isBeforeDeletedBase() ) {
                     indelString = String.format("D%d",p.getEventLength());
                     int cnt = consensusIndelStrings.containsKey(indelString)? consensusIndelStrings.get(indelString):0;
                     consensusIndelStrings.put(indelString,cnt+1);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index b787f8546..effcc39f0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -208,7 +208,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
 
     public class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
-            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletion(), PE.isAfterDeletion(), PE.isBeforeInsertion(), PE.isAfterInsertion(), PE.isNextToSoftClip());
+            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletedBase(), PE.isAfterDeletedBase(), PE.isBeforeInsertion(), PE.isAfterInsertion(), PE.isNextToSoftClip());
         }
 
         @Override
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 5a7e0f1c5..ea6901bb3 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -876,8 +876,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
     @Override
     public int getNumberOfDeletionsAfterThisElement() {
         int count = 0;
-        for (PileupElement p: this) {
-            if (p.isBeforeDeletion())
+        for (PileupElement p : this) {
+            if (p.isBeforeDeletionStart())
                 count++;
         }
         return count;
@@ -886,7 +886,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
     @Override
     public int getNumberOfInsertionsAfterThisElement() {
         int count = 0;
-        for (PileupElement p: this) {
+        for (PileupElement p : this) {
             if (p.isBeforeInsertion())
                 count++;
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 2eb81b394..771721169 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -24,8 +24,8 @@ public class PileupElement implements Comparable<PileupElement> {
     protected final GATKSAMRecord read;         // the read this base belongs to
     protected final int offset;                 // the offset in the bases array for this base
     protected final boolean isDeletion;         // is this base a deletion
-    protected final boolean isBeforeDeletion;   // is the base to the right of this base an deletion
-    protected final boolean isAfterDeletion;    // is the base to the left of this base a deletion
+    protected final boolean isBeforeDeletedBase;   // is the base to the right of this base an deletion
+    protected final boolean isAfterDeletedBase;    // is the base to the left of this base a deletion
     protected final boolean isBeforeInsertion;  // is the base to the right of this base an insertion
     protected final boolean isAfterInsertion;   // is the base to the left of this base an insertion
     protected final boolean isNextToSoftClip;   // is this base either before or after a soft clipped base
@@ -59,8 +59,8 @@ public class PileupElement implements Comparable<PileupElement> {
         this.read = read;
         this.offset = offset;
         this.isDeletion = isDeletion;
-        this.isBeforeDeletion = isBeforeDeletion;
-        this.isAfterDeletion = isAfterDeletion;
+        this.isBeforeDeletedBase = isBeforeDeletion;
+        this.isAfterDeletedBase = isAfterDeletion;
         this.isBeforeInsertion = isBeforeInsertion;
         this.isAfterInsertion = isAfterInsertion;
         this.isNextToSoftClip = isNextToSoftClip;
@@ -81,12 +81,20 @@ public class PileupElement implements Comparable<PileupElement> {
         return isDeletion;
     }
 
-    public boolean isBeforeDeletion() {
-        return isBeforeDeletion;
+    public boolean isBeforeDeletedBase() {
+        return isBeforeDeletedBase;
     }
 
-    public boolean isAfterDeletion() {
-        return isAfterDeletion;
+    public boolean isAfterDeletedBase() {
+        return isAfterDeletedBase;
+    }
+
+    public boolean isBeforeDeletionStart() {
+        return isBeforeDeletedBase && !isDeletion;
+    }
+
+    public boolean isAfterDeletionEnd() {
+        return isAfterDeletedBase && !isDeletion;
     }
 
     public boolean isBeforeInsertion() {