Unit tests for the context covariate

this is simple, but it's the infra-structure to start messing around with the context.

public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java

@@ -0,0 +1,103 @@
+package org.broadinstitute.sting.gatk.walkers.bqsr;
+
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.util.BitSet;
+import java.util.Random;
+
+/**
+ * Short one line description of the walker.
+ *
+ * <p>
+ * [Long description of the walker]
+ * </p>
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * [Description of the Input]
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * [Description of the Output]
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T [walker name]
+ *  </pre>
+ *
+ * @author Mauricio Carneiro
+ * @since 3/1/12
+ */
+public class ContextCovariateUnitTest {
+    ContextCovariate covariate;
+    RecalibrationArgumentCollection RAC;
+    Random random; 
+
+    @BeforeClass
+    public void init() {
+        RAC = new RecalibrationArgumentCollection();
+        covariate = new ContextCovariate();
+        random = GenomeAnalysisEngine.getRandomGenerator();
+        covariate.initialize(RAC);
+
+    }
+
+    @Test(enabled = true)
+    public void testSimpleContexts() {
+        byte [] quals = createRandomReadQuals(101);
+        byte [] bbases = createRandomReadBases(101);
+        String bases = stringFrom(bbases);
+        GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bbases, quals, bbases.length + "M");
+        CovariateValues values = covariate.getValues(read);
+        verifyCovariateArray((BitSet []) values.getMismatches(), RAC.MISMATCHES_CONTEXT_SIZE, bases);
+        verifyCovariateArray((BitSet []) values.getInsertions(), RAC.INSERTIONS_CONTEXT_SIZE, bases);
+        verifyCovariateArray((BitSet []) values.getDeletions(),  RAC.DELETIONS_CONTEXT_SIZE, bases);
+    }
+    
+    private void verifyCovariateArray(BitSet[] values, int contextSize, String bases) {
+        for (int i=0; i<values.length; i++) {
+            if (i >= contextSize)
+                Assert.assertEquals(MathUtils.dnaFrom(values[i]), bases.substring(i-contextSize, i));
+            else
+                Assert.assertNull(values[i]);
+        }
+    }
+
+    private String stringFrom(byte [] array) {
+        String s = "";
+        for (byte value : array)
+            s += (char) value;
+        return s;
+    }
+
+    private byte [] createRandomReadQuals(int length) {
+        byte [] quals = new byte[length];
+        for (int i=0; i<length; i++)
+            quals[i] = (byte) random.nextInt(50);
+        return quals;
+    }
+
+    private byte [] createRandomReadBases(int length) {
+        byte [] bases = new byte[length];
+        for (int i=0; i<length; i++) {
+            switch(random.nextInt(4)) {
+                case 0: bases[i] = 'A'; break;
+                case 1: bases[i] = 'C'; break;
+                case 2: bases[i] = 'G'; break;
+                case 3: bases[i] = 'T'; break;
+            }
+        }
+        return bases;
+    }
+}