Small refactoring: make Haplotype a public class since it will be soon extended and shared with other callers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4100 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.*;
 
 import java.util.*;
@@ -154,7 +155,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
 
             // Temp hack to match old implementation's scaling, TBD better behavior
 
-            return Arrays.asList(new Haplotype(haplotypeR.bases, 60), new Haplotype(haplotypeA.bases, contextSize));
+            return Arrays.asList(new Haplotype(haplotypeR.getBasesAsBytes(), 60), new Haplotype(haplotypeA.getBasesAsBytes(), contextSize));
         }
         else
             return null;
@@ -218,14 +219,14 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
             }
             else if ((chA == wc)) {
                 consensusChars[i] = chB;
-                consensusQuals[i] = haplotypeB.quals[i];
+                consensusQuals[i] = haplotypeB.getQuals()[i];
             }
             else if ((chB == wc)){
                 consensusChars[i] = chA;
-                consensusQuals[i] = haplotypeA.quals[i];
+                consensusQuals[i] = haplotypeA.getQuals()[i];
             } else {
                 consensusChars[i] = chA;
-                consensusQuals[i] = haplotypeA.quals[i]+haplotypeB.quals[i];
+                consensusQuals[i] = haplotypeA.getQuals()[i]+haplotypeB.getQuals()[i];
             }
 
 
@@ -289,7 +290,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
             if ( baseOffset >= read.getReadLength() )
                 break;
 
-            byte haplotypeBase = haplotype.bases[i];
+            byte haplotypeBase = haplotype.getBasesAsBytes()[i];
             byte readBase = read.getReadBases()[baseOffset];
 
             boolean matched = BaseUtils.basesAreEqual(readBase, haplotypeBase );
@@ -314,41 +315,6 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
             FLAT_BASE_PRIORS[i] = Math.log10(1.0 / BaseUtils.Base.values().length);
     }
 
-    private class Haplotype {
-        byte[] bases = null;
-        double[] quals = null;
-
-        /**
-         * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual
-         *
-         * @param bases bases
-         * @param qual  qual
-         */
-        Haplotype(byte[] bases, int qual) {
-            this.bases = bases;
-            quals = new double[bases.length];
-            Arrays.fill(quals, (double)qual);
-        }
-
-        Haplotype(byte[] bases, double[] quals) {
-            this.bases = bases;
-            this.quals = quals;
-        }
-
-        Haplotype(String bases, double[] quals) {
-            this.bases = bases.getBytes();
-            this.quals = quals;
-        }
-        public String toString() { return new String(this.bases); }
-
-        double getQualitySum() {
-            double s = 0;
-            for (int k=0; k < bases.length; k++) {
-                s += quals[k];
-            }
-            return s;
-        }
-    }
 
     public List<String> getKeyNames() { return Arrays.asList("HaplotypeScore"); }
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HaplotypeScore", 1, VCFHeaderLineType.Float, "Consistency of the site with two (and only two) segregating haplotypes")); }

java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java

@@ -0,0 +1,76 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.genotype;
+
+import java.util.Arrays;
+
+public class Haplotype {
+    protected byte[] bases = null;
+    protected double[] quals = null;
+
+    /**
+     * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual
+     *
+     * @param bases bases
+     * @param qual  qual
+     */
+    public Haplotype(byte[] bases, int qual) {
+        this.bases = bases;
+        quals = new double[bases.length];
+        Arrays.fill(quals, (double)qual);
+    }
+
+    public Haplotype(byte[] bases, double[] quals) {
+        this.bases = bases;
+        this.quals = quals;
+    }
+
+    public Haplotype(String bases, double[] quals) {
+        this.bases = bases.getBytes();
+        this.quals = quals;
+    }
+
+    public Haplotype(byte[] bases) {
+        this(bases, 0);
+    }
+
+
+    public String toString() { return new String(this.bases); }
+
+    public double getQualitySum() {
+        double s = 0;
+        for (int k=0; k < bases.length; k++) {
+            s += quals[k];
+        }
+        return s;
+    }
+
+    public double[] getQuals() {
+        return quals;
+    }
+    public byte[] getBasesAsBytes() {
+        return bases;
+    }
+}