From 611a395783c861f70b25157368045ffb257e762b Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 5 Nov 2011 12:18:56 -0400
Subject: [PATCH] Now properly extending candidate haplotypes with bases from
 the reference context instead of filling with padding bases. Functionality in
 the private Haplotype class is no longer necessary so removing it. No need to
 have four different Haplotype classes in the GATK.

---
 .../gatk/walkers/annotator/HaplotypeScore.java | 10 +++++-----
 .../indels/HaplotypeIndelErrorModel.java       | 18 +++++++++---------
 .../walkers/indels/PairHMMIndelErrorModel.java |  4 ++--
 .../broadinstitute/sting/utils/Haplotype.java  | 12 ++++++++----
 4 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index c142109fa..803bf514c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -180,12 +180,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
             final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
 
             List<Haplotype>hlist = new ArrayList<Haplotype>();
-            hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
+            hlist.add(new Haplotype(haplotype1.getBases(), 60));
 
             for (int k=1; k < haplotypesToCompute; k++) {
                 Haplotype haplotype2 = consensusHaplotypeQueue.poll();
                 if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
-                hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));
+                hlist.add(new Haplotype(haplotype2.getBases(), 20));
             }
             return hlist;
         } else
@@ -229,8 +229,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
     }
 
     private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
-        final byte[] a = haplotypeA.getBasesAsBytes();
-        final byte[] b = haplotypeB.getBasesAsBytes();
+        final byte[] a = haplotypeA.getBases();
+        final byte[] b = haplotypeB.getBases();
 
         if (a.length != b.length) {
             throw new ReviewedStingException("Haplotypes a and b must be of same length");
@@ -313,7 +313,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         // actually be a miscall in a matching direction, which would happen at a e / 3 rate.  If b != c, then
         // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
         // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
-        final byte[] haplotypeBases = haplotype.getBasesAsBytes();
+        final byte[] haplotypeBases = haplotype.getBases();
         final SAMRecord read = p.getRead();
         byte[] readBases = read.getReadBases();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 3b3f54b05..200a250f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (haplotypeIndex < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex];
+                    haplotypeBase = haplotype.getBases()[haplotypeIndex];
                 else
                     haplotypeBase = (byte)0; // dummy
 
@@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
                 if (readQual > 3)
                     pRead += pBaseRead;
                 haplotypeIndex++;
-                if (haplotypeIndex >= haplotype.getBasesAsBytes().length)
+                if (haplotypeIndex >= haplotype.getBases().length)
                     haplotypeIndex = RIGHT_ALIGN_INDEX;
                 //System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead);
              }
@@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
                 System.out.println(read.getReadName());
                 System.out.print("Haplotype:");
 
-                for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                for (int k=0; k <haplotype.getBases().length; k++) {
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
 
                 System.out.println("Haplotype:");
 
-                for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[indX-1];
+                    haplotypeBase = haplotype.getBases()[indX-1];
                 else
                     haplotypeBase = readBase;
 
@@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
             System.out.println(read.getReadName());
             System.out.print("Haplotype:");
 
-            for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
-                System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+            for (int k=0; k <haplotype.getBases().length; k++) {
+                System.out.format("%c ", haplotype.getBases()[k]);
             }
             System.out.println();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 11ff99ce3..b28980d9c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -381,7 +381,7 @@ public class PairHMMIndelErrorModel {
         // todo -- refactor into separate function
         for (Allele a: haplotypeMap.keySet()) {
             Haplotype haplotype = haplotypeMap.get(a);
-            byte[] haplotypeBases = haplotype.getBasesAsBytes();
+            byte[] haplotypeBases = haplotype.getBases();
             double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
             double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
 
@@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
                         long indStart = start - haplotype.getStartPosition();
                         long indStop =  stop - haplotype.getStartPosition();
 
-                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
+                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
                                 (int)indStart, (int)indStop);
 
                         double readLikelihood;
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index ce2ca2c28..df682f215 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -33,8 +33,8 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 public class Haplotype {
-    protected byte[] bases = null;
-    protected double[] quals = null;
+    protected final byte[] bases;
+    protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private boolean isReference = false;
  
@@ -69,6 +69,11 @@ public class Haplotype {
         this.isReference = isRef;
     }
 
+    @Override
+    public boolean equals( Object h ) {
+        return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
+    }
+
     public double getQualitySum() {
         double s = 0;
         for (int k=0; k < bases.length; k++) {
@@ -88,7 +93,7 @@ public class Haplotype {
     public double[] getQuals() {
         return quals;
     }
-    public byte[] getBasesAsBytes() {
+    public byte[] getBases() {
         return bases;
     }
 
@@ -100,7 +105,6 @@ public class Haplotype {
         return genomeLocation.getStop();
     }
 
-
     public boolean isReference() {
         return isReference;
     }