Added hidden mode for BQSR to force all read groups to be the same one.

* Very useful for debugging sample-specific issues
 * This argument got lost in the transition from BQSR v1 to v2
 * Added unit test to cover this case

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java

@@ -219,6 +219,10 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
     public String FORCE_PLATFORM = null;
 
+    @Hidden
+    @Argument(fullName = "force_readgroup", shortName = "fRG", required = false, doc = "If provided, the read group of EVERY read will be forced to be the provided String.")
+    public String FORCE_READGROUP = null;
+
     @Hidden
     @Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only", defaultToStdout = false)
     public PrintStream RECAL_TABLE_UPDATE_LOG = null;

protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java

@@ -93,10 +93,13 @@ public class ReadGroupCovariate implements RequiredCovariate {
     private final HashMap<String, Integer> readGroupLookupTable = new HashMap<String, Integer>();
     private final HashMap<Integer, String> readGroupReverseLookupTable = new HashMap<Integer, String>();
     private int nextId = 0;
+    private String forceReadGroup;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
     @Override
-    public void initialize(final RecalibrationArgumentCollection RAC) {}
+    public void initialize(final RecalibrationArgumentCollection RAC) {
+        forceReadGroup = RAC.FORCE_READGROUP;
+    }
 
     @Override
     public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
@@ -170,6 +173,9 @@ public class ReadGroupCovariate implements RequiredCovariate {
      * @return platform unit or readgroup id
      */
     private String readGroupValueFromRG(final GATKSAMReadGroupRecord rg) {
+        if ( forceReadGroup != null )
+            return forceReadGroup;
+
         final String platformUnit = rg.getPlatformUnit();
         return platformUnit == null ? rg.getId() : platformUnit;
     }

protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java

@@ -75,26 +75,37 @@ public class ReadGroupCovariateUnitTest {
         final String expected = "SAMPLE.1";
         GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("MY.ID");
         rg.setPlatformUnit(expected);
-        runTest(rg, expected);
+        runTest(rg, expected, covariate);
     }
 
     @Test(enabled = true)
     public void testMissingPlatformUnit() {
         final String expected = "MY.7";
         GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(expected);
-        runTest(rg, expected);
+        runTest(rg, expected, covariate);
     }
 
-    private void runTest(GATKSAMReadGroupRecord rg, String expected) {
+    @Test(enabled = true)
+    public void testForceReadgroup() {
+        final RecalibrationArgumentCollection forcedRAC = new RecalibrationArgumentCollection();
+        forcedRAC.FORCE_READGROUP = "FOO";
+        final ReadGroupCovariate forcedCovariate = new ReadGroupCovariate();
+        forcedCovariate.initialize(forcedRAC);
+
+        final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("NOT_FOO");
+        runTest(rg, "FOO", forcedCovariate);
+    }
+
+    private static void runTest(final GATKSAMReadGroupRecord rg, final String expected, final ReadGroupCovariate covariate) {
         GATKSAMRecord read = ReadUtils.createRandomRead(10);
         read.setReadGroup(rg);
         ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
         covariate.recordValues(read, readCovariates);
-        verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected);
+        verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected, covariate);
 
     }
 
-    private void verifyCovariateArray(int[][] values, String expected) {
+    private static void verifyCovariateArray(final int[][] values, final String expected, final ReadGroupCovariate covariate) {
         for (int[] value : values) {
             String actual = covariate.formatKey(value[0]);
             Assert.assertEquals(actual, expected);