A few more char -> byte cleanups

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java

@@ -53,6 +53,9 @@ public class ReferenceContext {
      */
     private byte[] bases;
 
+    /**
+     * A cache of the bases converted to characters for walkers not yet using byte[] interface
+     */
     private char[] basesAsCharCached = null;
 
     /**
@@ -64,6 +67,7 @@ public class ReferenceContext {
         this( locus, locus, new byte[] { base } );
     }
 
+    // todo -- this really should take the referenceview as an option and only grab the bases if necessary
     public ReferenceContext( GenomeLoc locus, GenomeLoc window, byte[] bases ) {
   //      if( !window.containsP(locus) )
   //          throw new StingException("Invalid locus or window; window does not contain locus");

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010.
+ * 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
@@ -12,15 +12,14 @@
  *
  * 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010.
+ * 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
@@ -12,15 +12,14 @@
  *
  * 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java

@@ -73,7 +73,7 @@ public class DiploidGenotypePriors {
      * @param ref
      * @param heterozygosity
      */
-    public DiploidGenotypePriors(char ref, double heterozygosity, boolean dontPolarize) {
+    public DiploidGenotypePriors(byte ref, double heterozygosity, boolean dontPolarize) {
         if ( dontPolarize ) {
             double[] vals = heterozygosity2DiploidProbabilities(heterozygosity);
             priors = getReferenceIndependentPriors(ref, vals[0], vals[1], vals[2]);
@@ -90,7 +90,7 @@ public class DiploidGenotypePriors {
      * @param heterozygosity
      * @param probOfTriStateGenotype The prob of seeing a true B/C het when the reference is A
      */
-    public DiploidGenotypePriors(char ref, double heterozygosity, double probOfTriStateGenotype) {
+    public DiploidGenotypePriors(byte ref, double heterozygosity, double probOfTriStateGenotype) {
         priors = getReferencePolarizedPriors(ref, heterozygosity, probOfTriStateGenotype);
     }
 
@@ -226,7 +226,7 @@ public class DiploidGenotypePriors {
      * @param heterozyosity
      * @param pRefError
      */
-    public static double[] getReferencePolarizedPriors(char ref, double heterozyosity, double pRefError ) {
+    public static double[] getReferencePolarizedPriors(byte ref, double heterozyosity, double pRefError ) {
         if ( ! MathUtils.isBounded(pRefError, 0.0, 0.01) ) {
             throw new RuntimeException(String.format("BUG: p Reference error is out of bounds (0.0 - 0.01) is allow range %f", pRefError));
         }
@@ -276,7 +276,7 @@ public class DiploidGenotypePriors {
      * @param priorHomVar
      */
     @Deprecated
-    public static double[] getReferenceIndependentPriors(char ref, double priorHomRef, double priorHet, double priorHomVar ) {
+    public static double[] getReferenceIndependentPriors(byte ref, double priorHomRef, double priorHet, double priorHomVar ) {
         if ((priorHomRef + priorHet + priorHomVar) != 1) {
             throw new RuntimeException(String.format("Prior probabilities don't sum to one => %f, %f, %f", priorHomRef, priorHet, priorHomVar));
         }
@@ -284,7 +284,7 @@ public class DiploidGenotypePriors {
         double[] priors = new double[DiploidGenotype.values().length];
 
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
-            int nRefBases = MathUtils.countOccurrences(ref, g.toString());
+            int nRefBases = MathUtils.countOccurrences((char)ref, g.toString());  // todo -- fixme
             double log10POfG = 0.0;
 
             switch ( nRefBases ) {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -215,7 +215,7 @@ public class UnifiedGenotyperEngine {
             if ( stratifiedContexts == null )
                 return null;
 
-            DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
+            DiploidGenotypePriors priors = new DiploidGenotypePriors((byte)ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
             call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors);
 
             // annotate the call, if possible

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -638,19 +638,19 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         }
     }
 
-    private String formatKeyword(String keyWord) {
+//    private String formatKeyword(String keyWord) {
-        //System.out.printf("keyword %s%n", keyWord);
+//        //System.out.printf("keyword %s%n", keyWord);
-
+//
-        StringBuilder s = new StringBuilder();
+//        StringBuilder s = new StringBuilder();
-        int i = 0;
+//        int i = 0;
-        for ( String part : keyWord.split("\\.") ) {
+//        for ( String part : keyWord.split("\\.") ) {
-            //System.out.printf("part %s %d%n", part, nameSizes[i]);
+//            //System.out.printf("part %s %d%n", part, nameSizes[i]);
-            s.append(String.format("%" + nameSizes[i] + "s ", part));
+//            s.append(String.format("%" + nameSizes[i] + "s ", part));
-            i++;
+//            i++;
-        }
+//        }
-
+//
-        return s.toString();
+//        return s.toString();
-    }
+//    }
 
     public void onTraversalDone(Integer result) {
         // our report mashaller

java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java

@@ -68,7 +68,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
         if (ref.getBase() == 'N' || ref.getBase() == 'n') return null; // we don't deal with the N ref base case
 
         ReadBackedPileup pileup = context.getPileup();
-        double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBaseAsChar(),
+        double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBase(),
                                                                                  DiploidGenotypePriors.HUMAN_HETEROZYGOSITY,
                                                                                  0.01);
         // get the bases and qualities from the pileup

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

@@ -47,22 +47,31 @@ public enum DiploidGenotype {
     GT ('G', 'T'),
     TT ('T', 'T');
 
-    public char base1, base2;
+    public byte base1, base2;
+
     private DiploidGenotype(char base1, char base2) {
+        this((byte)base1, (byte)base2);
+    }
+
+    private DiploidGenotype(byte base1, byte base2) {
         this.base1 = base1;
         this.base2 = base2;
     }
 
-    public boolean isHomRef(char r) {
+    public boolean isHomRef(byte r) {
         return isHom() && r == base1;
     }
 
-    public boolean isHomVar(char r) {
+    public boolean isHomVar(byte r) {
         return isHom() && r != base1;
     }
 
-    public boolean isHetRef(char r) {
+    public boolean isHetRef(byte r) {
-        return MathUtils.countOccurrences(r, this.toString()) == 1;
+        if ( base1 == r )
+            return r != base2;
+        else
+            return base2 == r;
+        //return MathUtils.countOccurrences(r, this.toString()) == 1;
     }
 
     public boolean isHom() {

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java

@@ -70,9 +70,9 @@ public class GenotypeLikelihoodsUnitTest extends BaseTest {
     private void testGenotypePriors(char ref, double h, double[] array) {
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
             double val = 0.0;
-            if ( g.isHomRef(ref) ) val = DiploidGenotypePriors.heterozygosity2HomRefProbability(h);
+            if ( g.isHomRef((byte)ref) ) val = DiploidGenotypePriors.heterozygosity2HomRefProbability(h);
             if ( g.isHet() )       val = DiploidGenotypePriors.heterozygosity2HetProbability(h);
-            if ( g.isHomVar(ref) ) val = DiploidGenotypePriors.heterozygosity2HomVarProbability(h);
+            if ( g.isHomVar((byte)ref) ) val = DiploidGenotypePriors.heterozygosity2HomVarProbability(h);
 
             val = log10(val);
             double e = array[g.ordinal()];
@@ -99,7 +99,7 @@ public class GenotypeLikelihoodsUnitTest extends BaseTest {
     }
 
     private void testPolarizedGenotypePriors(char ref, double h, double pRefError, double[] array) {
-        DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, h, pRefError);
+        DiploidGenotypePriors priors = new DiploidGenotypePriors((byte)ref, h, pRefError);
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
             double val = Math.pow(10, priors.getPrior(g));
             double e = array[g.ordinal()];