Adding the work-in-progress, experimental RepeatLengthCovariate to the BQSR so Chris can continue the development.

public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java

@@ -0,0 +1,64 @@
+package org.broadinstitute.sting.utils.recalibration.covariates;
+
+import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
+import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.TandemRepeat;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+
+import java.util.Arrays;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: rpoplin
+ * Date: 11/3/12
+ */
+
+public class RepeatLengthCovariate implements ExperimentalCovariate {
+    final int MAX_REPEAT_LENGTH = 20;
+
+    // Initialize any member variables using the command-line arguments passed to the walkers
+    @Override
+    public void initialize(final RecalibrationArgumentCollection RAC) {}
+
+    @Override
+    public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
+        byte[] readBytes = read.getReadBases();
+        for (int i = 0; i < readBytes.length; i++) {
+            int maxRL = 0;
+            for (int str = 1; str <= 8; str++) {
+                if (i + str <= readBytes.length) {
+                    maxRL = Math.max(maxRL, VariantContextUtils.findNumberofRepetitions(
+                            Arrays.copyOfRange(readBytes,i,i + str),
+                            Arrays.copyOfRange(readBytes,i,readBytes.length)
+                    ));
+                }
+            }
+            if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
+            values.addCovariate(maxRL, maxRL, maxRL, i);
+        }
+    }
+
+    // Used to get the covariate's value from input csv file during on-the-fly recalibration
+    @Override
+    public final Object getValue(final String str) {
+        return Byte.parseByte(str);
+    }
+
+    @Override
+    public String formatKey(final int key) {
+        return String.format("%d", key);
+    }
+
+    @Override
+    public int keyFromValue(final Object value) {
+        return (value instanceof String) ? Integer.parseInt((String) value) : (Integer) value;
+    }
+
+    @Override
+    public int maximumKeyValue() {
+        return MAX_REPEAT_LENGTH + 1;
+    }
+
+}

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java

@@ -1267,7 +1267,7 @@ public class VariantContextUtils {
      * @param testString             String to test
      * @return                       Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
      */
-    protected static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
+    public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
         int numRepeats = 0;
         for (int start = 0; start < testString.length; start += repeatUnit.length) {
             int end = start + repeatUnit.length;