oops - we don't need reference bases, but we still need reference

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1653 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java

@@ -27,7 +27,7 @@ import java.util.*;
  * Copies reads from the input stream into the <code>outputBAM</code>, replacing those
  * reads which have been cleaned with their new clean copies.
  */
-@Requires({DataSource.READS})
+@Requires({DataSource.READS, DataSource.REFERENCE})
 public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
 
     /**

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java

@@ -16,7 +16,7 @@ import java.util.List;
 // although this can easily be changed if necessary.
 
 @WalkerName("IndelIntervals")
-@Requires({DataSource.READS})
+@Requires({DataSource.READS, DataSource.REFERENCE})
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> {
     @Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)

java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java

@@ -39,7 +39,7 @@ import java.util.*;
  * Merges intervals based on reads which overlap them.
  */
 @WalkerName("IntervalMerger")
-@Requires({DataSource.READS})
+@Requires({DataSource.READS, DataSource.REFERENCE})
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java

@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 @WalkerName("SNPClusters")
-@Requires(value={},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)})
+@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)})
 public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
     @Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false)
     int windowSize = 10;