Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.

-- Removed REFERENCE_BASES option.  You only have REFERENCE now.  There's no efficiency savings for the REFERENCE_BASES option any longer, since the reference bases are loaded lazy so if you don't use them there's effectively no cost to making the RefContext that could load them.

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

@@ -75,8 +75,6 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
         if( !dataProvider.hasReads() )
             throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");
 
-        boolean needsReferenceBasesP = WalkerManager.isRequired(walker, DataSource.REFERENCE_BASES);
-
         ReadView reads = new ReadView(dataProvider);
         ReadReferenceView reference = new ReadReferenceView(dataProvider);
 
@@ -91,7 +89,7 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
             ReferenceContext refContext = null;
 
             // get the array of characters for the reference sequence, since we're a mapped read
-            if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
+            if (!read.getReadUnmappedFlag() && dataProvider.hasReference())
                 refContext = reference.getReferenceContext(read);
 
             // update the number of reads we've seen

public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java

@@ -28,7 +28,7 @@ import java.util.List;
  */
 
 @By(DataSource.READS)
-@Requires({DataSource.READS, DataSource.REFERENCE_BASES})
+@Requires({DataSource.READS, DataSource.REFERENCE})
 @PartitionBy(PartitionType.READ)
 @ActiveRegionExtension(extension=50,maxRegion=1500)
 @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class})

public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java

@@ -16,8 +16,18 @@ package org.broadinstitute.sting.gatk.walkers;
  * Allow user to choose between a number of different data sources.
  */
 public enum DataSource {
+    /**
+     * Does this walker require read (BAM) data to work?
+     */
     READS,
+
+    /**
+     * Does this walker require reference data to work?
+     */
     REFERENCE,
-    REFERENCE_BASES,         // Do I actually need the reference bases passed to the walker?
+
+    /**
+     * Does this walker require reference order data (VCF) to work?
+     */
     REFERENCE_ORDERED_DATA
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -16,7 +16,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.READS)
-@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
+@Requires({DataSource.READS,DataSource.REFERENCE})
 @PartitionBy(PartitionType.LOCUS)
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
 @RemoveProgramRecords

public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java

@@ -12,7 +12,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-@Requires({DataSource.READS, DataSource.REFERENCE_BASES})
+@Requires({DataSource.READS, DataSource.REFERENCE})
 @PartitionBy(PartitionType.READ)
 public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     public boolean requiresOrderedReads() { return false; }

public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java

@@ -8,7 +8,7 @@ package org.broadinstitute.sting.gatk.walkers;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.REFERENCE)
-@Requires({DataSource.REFERENCE, DataSource.REFERENCE_BASES})
+@Requires({DataSource.REFERENCE})
 @Allows(DataSource.REFERENCE)
 public abstract class RefWalker<MapType, ReduceType> extends LocusWalker<MapType, ReduceType> {
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -107,7 +107,7 @@ import java.util.ArrayList;
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By(DataSource.READS)
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class})                                   // only look at covered loci, not every loci of the reference file
-@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES})                                         // filter out all reads with zero or unavailable mapping quality
+@Requires({DataSource.READS, DataSource.REFERENCE})                                         // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS)                                                                                       // this walker requires both -I input.bam and -R reference.fasta
 public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
     @ArgumentCollection