Merged bug fix from Stable into Unstable

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

@@ -274,6 +274,38 @@ public class GenomeAnalysisEngine {
         //return result;
     }
 
+    // TODO -- Let's move this to a utility class in unstable - but which one?
+    // **************************************************************************************
+    // *                            Handle Deprecated Walkers                               *
+    // **************************************************************************************
+
+    // Mapping from walker name to major version number where the walker first disappeared
+    private static Map<String, String> deprecatedGATKWalkers = new HashMap<String, String>();
+    static {
+        deprecatedGATKWalkers.put("CountCovariates", "2.0");
+        deprecatedGATKWalkers.put("TableRecalibration", "2.0");
+    }
+
+    /**
+     * Utility method to check whether a given walker has been deprecated in a previous GATK release
+     *
+     * @param walkerName   the walker class name (not the full package) to check
+     */
+    public static boolean isDeprecatedWalker(final String walkerName) {
+        return deprecatedGATKWalkers.containsKey(walkerName);
+    }
+
+    /**
+     * Utility method to check whether a given walker has been deprecated in a previous GATK release
+     *
+     * @param walkerName   the walker class name (not the full package) to check
+     */
+    public static String getDeprecatedMajorVersionNumber(final String walkerName) {
+        return deprecatedGATKWalkers.get(walkerName);
+    }
+
+    // **************************************************************************************
+
     /**
      * Retrieves an instance of the walker based on the walker name.
      *
@@ -287,6 +319,9 @@ public class GenomeAnalysisEngine {
             if ( isGATKLite() && GATKLiteUtils.isAvailableOnlyInFullGATK(walkerName) ) {
                 e = new UserException.NotSupportedInGATKLite("the " + walkerName + " walker is available only in the full version of the GATK");
             }
+            else if ( isDeprecatedWalker(walkerName) ) {
+                e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
+            }
             throw e;
         }
     }

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

@@ -316,9 +316,9 @@ public class UserException extends ReviewedStingException {
 
 
 
-    public static class MissingWalker extends UserException {
+    public static class DeprecatedWalker extends UserException {
-        public MissingWalker(String walkerName, String message) {
+        public DeprecatedWalker(String walkerName, String version) {
-            super(String.format("Walker %s is not available: %s", walkerName, message));
+            super(String.format("Walker %s is no longer available in the GATK; it has been deprecated since version %s", walkerName, version));
         }
     }
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala

@@ -347,6 +347,7 @@ class DataProcessingPipeline extends QScript {
     this.knownSites ++= qscript.dbSNP
     this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
+    this.disable_indel_quals = true
     this.out = outRecalFile
     if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
     if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
@@ -359,7 +360,6 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.BQSR = inRecalFile
-    this.disable_indel_quals = true
     this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala

@@ -166,6 +166,7 @@ class PacbioProcessingPipeline extends QScript {
     this.knownSites :+= dbSNP
     this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
+    this.disable_indel_quals = true
     this.out = outRecalFile
     this.analysisName = queueLogDir + outRecalFile + ".covariates"
     this.jobName = queueLogDir + outRecalFile + ".covariates"
@@ -178,7 +179,6 @@ class PacbioProcessingPipeline extends QScript {
     this.input_file :+= inBam
     this.BQSR = inRecalFile
     this.out = outBam
-    this.disable_indel_quals = true
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"