1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.

protected/java/src/org/broadinstitute/sting/utils/DummyProtectedClass.java

@@ -0,0 +1,34 @@
+package org.broadinstitute.sting.utils;
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
+
+public class DummyProtectedClass implements ProtectedPackageSource {
+
+    // THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK
+
+}

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java

@@ -104,10 +104,10 @@ public class BQSRIntegrationTest extends WalkerTest {
     @DataProvider(name = "PRTest")
     public Object[][] createPRTestData() {
         return new Object[][]{
-                {new PRTest("", "66aa65223f192ee39c1773aa187fd493")},
+                {new PRTest("", "d2d6ed8667cdba7e56f5db97d6262676")},
-                {new PRTest(" -qq -1 -IQ", "b7053d3d67aba6d8892f0a60f0ded338")},
+                {new PRTest(" -qq -1", "b7053d3d67aba6d8892f0a60f0ded338")},
-                {new PRTest(" -qq 6 -IQ", "bfbf0855185b2b70aa35237fb71e4487")},
+                {new PRTest(" -qq 6", "bfbf0855185b2b70aa35237fb71e4487")},
-                {new PRTest(" -IQ", "d2d6ed8667cdba7e56f5db97d6262676")}
+                {new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")}
         };
     }
 

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -51,6 +51,7 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -197,17 +198,28 @@ public class GenomeAnalysisEngine {
     private BaseRecalibration baseRecalibration = null;
     public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
     public boolean hasBaseRecalibration() { return baseRecalibration != null; }
-    public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean useIndelQuals, final int preserveQLessThan) {
+    public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
-        baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, useIndelQuals, preserveQLessThan, isGATKLite());
+        baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, isGATKLite());
     }
 
     /**
      * Utility method to determine whether this is the lite version of the GATK
      */
     public boolean isGATKLite() {
-        // TODO -- this is just a place holder for now
+        if ( isLiteVersion == null ) {
-        return false;
+            final List<Class<? extends Object>> classes = new PluginManager<Object>(Object.class).getPlugins();
+            isLiteVersion = true;
+            for ( Class c : classes ) {
+                if ( c.getSimpleName().equals(DummyProtectedClassName)) {
+                    isLiteVersion = false;
+                    break;
+                }
+            }
+        }
+        return isLiteVersion;
     }
+    private static final String DummyProtectedClassName = "DummyProtectedClass";
+    private static Boolean isLiteVersion = null;
 
     /**
      * Actually run the GATK with the specified walker.
@@ -239,7 +251,7 @@ public class GenomeAnalysisEngine {
 
         // if the use specified an input BQSR recalibration table then enable on the fly recalibration
         if (args.BQSR_RECAL_FILE != null)
-            setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.enableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN);
+            setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN);
 
         // Determine how the threads should be divided between CPU vs. IO.
         determineThreadAllocation();

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -215,10 +215,10 @@ public class GATKArgumentCollection {
     public int quantizationLevels = 0;
 
     /**
-     * Turns on printing of the base insertion and base deletion tags when using the -BQSR argument.  By default, only the base substitution qualities will be produced.
+     * Turns off printing of the base insertion and base deletion tags when using the -BQSR argument and only the base substitution qualities will be produced.
      */
-    @Argument(fullName="enable_indel_quals", shortName = "IQ", doc = "If true, enables printing of base insertion and base deletion tags (with -BQSR)", required=false)
+    @Argument(fullName="disable_indel_quals", shortName = "DIQ", doc = "If true, disables printing of base insertion and base deletion tags (with -BQSR)", required=false)
-    public boolean enableIndelQuals = false;
+    public boolean disableIndelQuals = false;
 
     /**
      * Do not modify quality scores less than this value but rather just write them out unmodified in the recalibrated BAM file.

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -79,8 +79,8 @@ public class UserException extends ReviewedStingException {
     }
 
     public static class NotSupportedInGATKLite extends UserException {
-        public NotSupportedInGATKLite(String argument) {
+        public NotSupportedInGATKLite(String message) {
-            super(String.format("Unfortunately, the argument %s is not supported in the Lite version of the GATK", argument));
+            super(String.format("GATK Lite does support all of the features of the full version: %s", message));
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

@@ -50,7 +50,7 @@ public class BaseRecalibration {
     private final RecalibrationTables recalibrationTables;
     private final Covariate[] requestedCovariates;                                                                      // list of all covariates to be used in this calculation
 
-    private final boolean emitIndelQuals;
+    private final boolean disableIndelQuals;
     private final int preserveQLessThan;
 
     private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
@@ -64,14 +64,14 @@ public class BaseRecalibration {
      * 
      * @param RECAL_FILE         a GATK Report file containing the recalibration information
      * @param quantizationLevels number of bins to quantize the quality scores
-     * @param emitIndelQuals     if true, emit base indel qualities
+     * @param disableIndelQuals  if true, do not emit base indel qualities
      * @param preserveQLessThan  preserve quality scores less than this value
      * @param isGATKLite         is this being called from the full or Lite version of the GATK
      */
-    public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean emitIndelQuals, final int preserveQLessThan, final boolean isGATKLite) {
+    public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean isGATKLite) {
         // check for unsupported access
-        if (isGATKLite && emitIndelQuals)
+        if (isGATKLite && !disableIndelQuals)
-            throw new UserException.NotSupportedInGATKLite("enable_indel_quals");
+            throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
 
         RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
 
@@ -84,7 +84,7 @@ public class BaseRecalibration {
             quantizationInfo.quantizeQualityScores(quantizationLevels);
 
         readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
-        this.emitIndelQuals = emitIndelQuals;
+        this.disableIndelQuals = disableIndelQuals;
         this.preserveQLessThan = preserveQLessThan;
     }
 
@@ -98,7 +98,7 @@ public class BaseRecalibration {
     public void recalibrateRead(final GATKSAMRecord read) {
         RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates);                                  // compute all covariates for the read
         for (final EventType errorModel : EventType.values()) {                                                         // recalibrate all three quality strings
-            if (!emitIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
+            if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
                 read.setBaseQualities(null, errorModel);
                 continue;
             }